From bronze!news.cs.indiana.edu!ux1.cso.uiuc.edu!uxh.cso.uiuc.edu!lwalsh Sat Dec 7 18:25:32 EST 1991 Article: 175 of bionet.molbio.proteins Newsgroups: bionet.molbio.proteins Path: bronze!news.cs.indiana.edu!ux1.cso.uiuc.edu!uxh.cso.uiuc.edu!lwalsh From: lwalsh@uxh.cso.uiuc.edu (Laura Lynn Walsh) Subject: PDB info file Message-ID: <1991Dec7.223437.9496@ux1.cso.uiuc.edu> Sender: usenet@ux1.cso.uiuc.edu (News) Organization: University of Illinois at Urbana Date: Sat, 7 Dec 1991 22:34:37 GMT Lines: 1549 I have compiled a crossreference of the Brookhaven Protein Data Bank files which may be of use to others. If you find errors in this listing please let me know. /* This file was compiled by Laura Lynn Walsh, Beckman Institute, University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801-2325 (217) 244-6764 lwalsh@nemo.life.uiuc.edu Date begun: November, 1990 Latest revision: November, 1991 This file is an annotation of all of the Brookhaven Protein Data Bank files with actual coordinates. (The files beginning with pdb0 have been omitted until full coordinates are available.) The information has been taken from the Brookhaven Protein Data Bank and from original papers by authors listed in those files. Responsibility for the accuracy of the information is LLW's, who would welcome reports of errors and suggestions to extend the usefulness of the information. This information is provided for your use and no warranty about the correctness of the infor- mation is made. Support from NSF-DIR90-19063 for LLW is gratefully acknowledged. */ /* Description of Entries: The header line begins with the common name for the protein or other molecule(s) contained in the file.I have tried to use the most commonly accepted names, but in several cases, especially the immunoglobulin files, this has been difficult. The molecule name is followed by its source. This is the source of the original sequence.In several cases a protein is actually expressed in another organism, such as E. coli, but this is not noted in this file. DUP = duplicate entry. This file is also listed for another protein or other molecule. (E.g. the Eglin C and subtilisin complex is listed under both headers.) The file names from the Brookhaven Protein Data Bank have been abbreviated. Where Brookhaven names the files pdbXXXX.ent, the files are referred to here solely by the XXXX part. Files with a "w" appended to their names are files that I have modified to make a "complete" protein, i.e., if the protein is a tetramer and only two of the chains are given in the original file, the new file would contain the tetramer and conversely, if the original file contains two chains and the protein is a monomer, this file contains a single chain. These files are not publicly available at present. The columns following the PDB file name indicate the resolution for the x-ray data. If the file is an NMR file, "NMR" is in this field, since resolution is not applicable for these. "CA" indicates that the entry contains coordinate information only for the alpha carbons. "UNK" means the amino acid sequence is unknown. The body of the entry indicates how many chains are in the "complete" molecule (see below), how many chains are included in the entry, and any other information that helps distinguish that specific entry from another similar entry. I have also included any information I had that could help in interpreting the data in the entry.In particular, I have attempted to include any possible differences between the crystallographic data and what is thought to be the active, "solution" structure of the molecule. I am currently working on including information about ions and crystallization conditions, but this information should be considered incomplete. */ /* "Correct" proteins are either the complete protein as seen in the pictures accompanying the original literature or, failing this, a protein that "looks ok" and which can be generated by both my program and Insight (Biosym) to look the same. Failing both of these, a correct protein is as close as I could come to what I think is correct. If it is not, PLEASE let me know. The "correct" proteins were generated by one of several possible methods: 1) If there was a matrix given in the data file itself which produced a "correct" protein, this was used. 2) If there was no applicable matrix, or if the matrix did not generate a correct protein, the International Table for Crystallography matrices were used. If possible, these were checked against the matrices and proteins produced by Insight (Biosym). Insight (Biosym) can do symmetry operations in its Assembly module under the Symmetry command. The program uses a 4 X 4 matrix and is thus not the same as the program I use to make symmetry related protein chains. I use a 3 X 4 matrix. I prefer my program for two reasons -- the atom numbering used in the original file is retained and the symmetry related chains are numbered 10000 more than the original atoms. This requires renumbering when there are several symmetry operations performed, but it makes generating CONECT records much easier. */ 434 Cro Protein (Phage 434) 2cro 2.35 monomer in solution - 1 chain given; dimer in crystal, but dimerizes differently when bound to DNA; Insight can't find space group R 32; includes water 434 Repressor Protein - N Terminal Domain (Phage 434) 1r69 2.0 monomer in solution - 1 chain given; includes water 2or1 2.5 dimer in complex with dsDNA (a2 + d2) - 4 chains given Acid Proteinase Endothiapepsin (Endothia parasitica) 4ape 2.1 monomer; sequence numbering based on pepsin; includes water 2er0 3.0 monomer; complex with inhibitor 2er6 2.0 monomer; complex with inhibitor 2er7 1.6 monomer; complex with inhibitor 2er9 2.2 monomer; complex with inhibitor 4er1 2.0 monomer; complex with inhibitor 4er2 2.0 monomer; complex with inhibitor 5er1 2.0 monomer; complex with inhibitor Acid Proteinase Penicillopepsin (Penicillium janthinellum) 2app 1.8 monomer 3app 1.8 monomer; supersedes 2app; includes water Acid Proteinase Rhizopuspepsin (Rhizopus chinensis) 2apr 1.8 monomer; supersedes 1apr; includes Ca++ 3apr 1.8 monomer; complex with reduced peptide inhibitor 4apr 2.5 monomer; complex with a pepstatin-like renin inhibitor 5apr 2.1 monomer; complex with a pepstatin-like renin inhibitor 6apr 2.5 monomer; complex with pepstatin Aconitase (Sus scrofa) 5acn 2.1 monomer; inactive 3Fe-4S form 6acn 2.5 monomer; active 4Fe-4S form; includes sulfate, tricar- ballylic acid and water Actinidin (Actinidia chinensis) 2act 1.7 monomer; supersedes 1act; includes oxygens, ammonium, and water Actinoxanthin (Actinomyces globisporus, number 1131) 1acx 2.0 monomer Adenylate Kinase (Sus scrofa) 3adk 2.1 monomer; supersedes 2adk; includes sulfates Agarose (Rhodophycae) 1aga 3.0 sugar polymer; NOT PROTEIN Alamethicin (Trichoderma viride) 1amt 1.5 3 chains given; contains many AIBs & 3 PHLs Alcohol Dehydrogenase (Equus caballus) 5adh 2.9 dimer (a2) - 1 chain given; apo; complex with ADP-ribose 6adh 2.9 dimer (a2) - 2 chains given; holo; complex with NAD & DMSO 7adh 3.2 dimer (a2) - 2 chains given; isonicotinamidylated 8adh 2.4 dimer (a2) - 1 chain given; apo 8adhw dimerized acc to included matrix Alpha-Amylase Inhibitor HOE-467A (Streptomyces tendae, 4158) 1hoe 2.0 monomer Alpha-Lytic Protease (Lysobacter enzymogenes) 1p01 2.0 complex with substrate analogs 1p02 2.0 complex with substrate analogs 1p03 2.15 complex with substrate analogs 1p04 2.55 complex with substrate analogs 1p05 2.10 complex with substrate analogs 1p06 2.34 complex with substrate analogs 1p07 2.25 complex with substrate analogs 1p08 2.25 complex with substrate analogs 1p09 2.20 complex with substrate analogs 1p10 2.25 complex with substrate analogs 2alp 1.7 monomer; gaps in numbering Alpha-1 Proteinase Inhibitor (Homo sapiens) Cleavage of original monomer yields 2 or 3 chains - 3rd "chain" is a single Cys residue. 5api 3.0 2 chains given; modified; bond cleavage results in large structural change; superseded by 7api 6api 3.0 2 chains given; modified; bond cleavage results in large structural change; active structure may be quite different; superseded by 8api 7api 3.0 3 chains given; modified; structural change; tetragonal form 1; supersedes 5api 8api 3.1 3 chains given; modified; structural change; hexagonal form; supersedes 6api 9api 3.0 3 chains given; modified; structural change; tetragonal form 2 Apolipoprotein D (Homo sapiens) 1apd --- model; non-experimental L-Arabinose binding protein (Escherichia coli) 1abp 2.4 monomer Aspartate Aminotransferase (Gallus gallus) 1aat 2.8 CA complex with 2-oxo-glutaric acid Aspartate Aminotransferase (Escherichia coli) 2aat 2.8 dimer (a2) - 1 chain given; mutant K258A; complex with pyridoxamine phosphate; 2aatw made; checked on Iris Aspartate Carbamoyltransferase (Escherichia coli) 2atc 3.0 dodecamer (3[a2b2]) - 2 chains given; unliganded 4atc 2.6 dodecamer (3[a2b2]) - 4 chains given; unliganded; superseded by 6at1 7atc 2.6 dodecamer (3[a2b2]) - 4 subunits; complex with CTP; supersedes 5atc; superseded by 5at1 8atc 2.5 dodecamer (3[a2b2]) - 4 chains given; R state; complex with PALA 1at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state; complex with PAM & MAL 2at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state; complex with PAM & MAL 3at1 2.8 dodecamer (3[a2b2]) - 4 chains given; T state; complex with PAM 4at1 2.6 dodecamer (3[a2b2]) - 4 chains given; T state; complex with ATP 5at1 2.6 dodecamer (3[a2b2]) - 4 chains given; T state; complex with CTP; supersedes 7atc 6at1 2.6 dodecamer (3[a2b2]) - 4 chains given; T state; supersedes 4atc 7at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state; complex with PAM, MAL, & ATP 8at1 2.8 dodecamer (3[a2b2]) - 4 chains given; R state; complex with PAM, MAL, & CTP ATX 1A (Anemonia sulcata) 1atx NMR monomer - 8 chains given; lowest energy conformation is model 1 Azurin (Alcaligenes denitrificans) 2aza 1.8 monomer - 2 chains given; oxidized 2azaw half of coords eliminated; monomer remains; there are a lot of contacts between the independent molecules in the crystal Azurin (Pseudomonas aeruginosa) 1azu 2.7 monomer Bacteriochlorophyll-A Protein (Prosthecochloris aestuarii, strain 2K) 3bcl 1.9 monomer; many UNK residues; all ASP & ASN are ASX; all GLU & GLN are GLX Bacteriorhodopsin (Halobacterium halobium) 1brd 3.5* monomer; resolution 3.5 in x and y directions, 10.0 in z BDS-1 (Anemonia sulcata) 1bds NMR monomer; averaged structure 2bds NMR monomer - 42 simulated annealing structures Bean Pod Mottle Virus - Middle Component (Bountiful bean) 1bmv 3.0 120mer + RNA (60ab + r) - 3 chains given; unusual numbering system; Insight can't find space group P 2 21 21 Alpha Bungarotoxin (Bungarus multicinctus) related to Cobratoxin 2abx 2.5 dimer (a2) - 2 chains given; due to crystal contacts, Phe sticks out into solvent - near to another Phe in a neighboring molecule Calcium-Binding Parvalbumin B (Cyprinus carpio) 1cdp 1.6 monomer; Cadmium substituted 1cpv 1.85 monomer 2cpv 1.85 monomer 3cpv 1.85 monomer 4cpv 1.5 monomer; pI 4.25 5cpv 1.6 monomer; supersedes 1cpv, 2cpv, 3cpv; due to crystal contacts, phe sticks out into solvent - near to another phe in a neighboring molecule Calcium-Binding Protein (Bos taurus) 3icb 2.3 monomer; supersedes 2icb; Calmodulin (Bos taurus) 2cln --- trimethyl Cln complex with trifluroperazine; non-exp'l model 3cln 2.2 monomer Carbonic Anhydrase I, Form B (Carbonate Dehydratase) (Homo sapiens) 2cab 2.0 monomer Carbonic Anhydrase II (Homo sapiens) 1ca2 2.0 monomer 2ca2 1.9 monomer; complex with thiocyanate ion 3ca2 2.0 monomer; complex with AMS Carboxypeptidase A (Bos taurus) 3cpa 2.0 monomer; alpha; complex with glycyl-L-tyrosine 4cpa 2.5 monomer; alpha; complex with inhibitor 5cpa 1.54 monomer; alpha Carboxypeptidase B (Bos taurus) 1cpb 2.8 CA monomer; fraction II D-Alanyl-D-Alanine Carboxypeptidase/Transpeptidase (Streptomyces r61) 1pte 2.8 CA seq uncertain Capsular Polysaccharide (Escherichia coli) 1cap 3.0 from mutant; NOT PROTEIN Cardiotoxin V4 (Naja mossambica mossambica) 1cdt 2.5 2 chains given Catabolite Gene Activator Protein (Escherichia coli) 2gap --- complex; model 3gap 2.5 dimer (a2) - 2 chains given - have diff configurations; complex with cyclic AMP Catalase (Penicillium vitale) 4cat 3.0 all residues listed as UNK Catalase (Bos taurus) 7cat 2.5 tetramer (a4) - 1 chain given 8cat 2.5 tetramer (a4) - 2 chains given 8catw tetramerized acc. to instructions; doesn't correspond to any replicate generated by Insight and matrix does not correspond to one in the International Tables; literature does not show picture of complete molecule CD4 (Homo sapiens) 1cd4 2.3 monomer; N-terminal fragment Cellobiohydrolase I (C terminal domain) (Trichoderma reesei) 1cbh NMR monomer; averaged structure 2cbh NMR 41 structures; simulated annealing Cellobiohydrolase II Core Protein (Trichoderma reesei) 3cbh 2.0 CA dimer (a2) - 1 chain given Che-Y (Salmonella typhimurium) 2chy 2.7 CA monomer; mutant (S56C) Chloramphenicol Acetyltransferase - Type III (Escherichia coli) 1cla 2.34 trimer (a3) - 1 chain given; mutant (S148A) 2cla 2.35 trimer (a3) - 1 chain given; mutant (D199N) 3cla 1.75 trimer (a3) - 1 chain given; complex with chloramphenicol 3claw trimerized acc. to included matrices; checked on Iris Chondroitin-4-Sulfate (Bos taurus) 1c4s 3.0 NOT PROTEIN 2c4s complex; NOT PROTEIN Chymosin B (Bos taurus) 1cms 2.3 monomer; crystal packing as done by Insight doesn't look like crystal packing in literature -- I: molecules are back to back; L: molecules are front to back Chymotrypsin Alpha (Bos taurus) same seq as gamma 1cho 1.8 monomer + inhibitor (a + b) - 2 chains given; complex with ovomucoid 3rd domain (inhibitor) 2cha 2.0 monomer; tosylated; EXC codes for excised residues 4cha 1.68 monomer - 2 chains given; EXC codes for excised residues 5cha 1.67 "dimeric structural unit" - 2 chains given; same as for 4cha 6cha 1.8 "dimeric structural unit" - 2 chains given; complex with PEBA Chymotrypsin Gamma (Bos taurus) same seq as alpha 2gch 1.9 monomer 3gch 1.9 monomer; with cinnamate 4gch 1.9 monomer; with cinnamate 5gch 2.7 monomer; photolysis product of inhibited molecule 6gch 2.1 monomer; with inhibitor APF 7gch 1.8 monomer; with inhibitor LF Chymotrypsin Inhibitor 2 (Hordeum vulgare, hiproly strain) 2ci2 2.0 monomer Chymotrypsinogen A (Bos taurus) 1chg 2.5 monomer; alpha; zymogen 2cga 1.8 monomer - 2 chains given; alpha; zymogen; extensive contacts between monomers 2cgaw half of coords eliminated; monomer remains Citrate Synthase (Gallus gallus) 3cts 1.7 UNKdimer (a2) - 1 chain given; complex with CO-A & citrate; residues all UNK; 5cts 1.9 dimer (a2) - 1 chain given; complex with oxaloacetate & CO-A; seq inferred from Sus scrofa (4cts); same form as 2cts, presumably monoclinic, closed 5ctsw made; checked on Iris; has protruding N-terminus in contact with neighboring dimer 6cts 2.5 dimer (a2) - 1 chain given; complex with citrylthioether & CO-A; seq as 5cts Citrate Synthase (Sus scrofa) 1cts 2.7 dimer (a2) - 1 chain given; complex with citrate 2cts 2.0 dimer (a2) - 1 chain given; complex with CO-A & citrate; monoclinic form (closed) 2ctsw dimer made; checked on Iris; has protruding N-terminus in contact with neighboring dimer 4cts 2.9 dimer (a2) - 2 chains given; complex with oxaloacetate & CO-A; tetragonal form (open) Alpha Cobratoxin (Naja naja siamensis) related to Bungarotoxin 1ctx 2.8 monomer Concanavalin A (Canavalia ensiformis) 1cn1 3.2 dimer (a2) - 2 chains given; demetallized 2cna 2.0 dimer or tetramer (a2 or a4) - 1 chain given 2cnaw made; checked 3cna 2.4 dimer or tetramer (a2 or a4) - 1 chain given Crambin (Crambe abyssinica) 1crn 1.5 monomer Cro Repressor Protein (Phage lambda) 1cro 2.2 CA 4 chains in data set (O,A,B,C); O-B thought to be functional unit Crystallin Gamma II (Bos taurus) 1gcr 1.6 monomer Crystallin Gamma IV (Bos taurus) 2gcr 2.3 monomer; but packs tightly in vivo under some conditions Cucumber Basic Protein (Cucumis sativus) 1cbp 2.5 CA C-AMP Dependent Protein Kinase (Bos primigenius Taurus) 1apk --- model of Type I - Domain A 2apk --- model of Type I - Domain A 1bpk --- model of Type I - Domain B 2bpk --- model of Type I - Domain B Cytochrome B5 (Bos taurus) membrane binding tail removed 2b5c 2.0 monomer; oxidized 3b5c 1.5 monomer; oxidized; supersedes 2b5c Cytochrome B562 (Escherichia coli) 156b 2.5 monomer; oxidized 256b 1.4 monomer - 2 chains given; oxidized; supersedes 156b 256bw made; checked Cytochrome C (Katsuwonis pelamis, linnaeus or Thunnus alalunga) seq same in T. alalunga & K. pelamis; Thunnus acetylated at N terminus 1cyc 2.3 monomer; ferro; Katsuwonis 3cyt 1.8 dimer (a2) - 2 chains given; oxidized; Thunnus 5cyt 1.5 monomer; reduced; Thunnus Cytochrome C (Oryza sativa l.) 1ccr 1.5 monomer Cytochrome C - Isozyme 1 (Saccharomyces cerevisiae) 1ycc 1.23 monomer?; reduced; one residue is actually trimethyllysine Cytochrome C Peroxidase (Saccharomyces cerevisiae) 2cyp 1.7 monomer 1ccp 2.2 monomer; native + two N-terminal aa's from expression in E.coli; sequence differs from 2cyp at 2 aa's -- strain-related 2ccp 2.2 monomer; D235N mutant of 1ccp 3ccp 2.2 monomer; W191F mutant of 1ccp 4ccp 2.2 monomer; W51F mutant of 1ccp Cytochrome C Prime (Rhodospirillum molischianum) 2ccy 1.67 dimer (a2) - 2 chains given Cytochrome C2 (Rhodospirillum rubrum) 2c2c 2.0 monomer; oxidized 3c2c 1.68 monomer; reduced Cytochrome C3 (Desulfovibrio desulfuricans Norway) 1cy3 2.5 monomer Cytochrome C3 (Desulfovibrio vulgaris miyazaki iam 12604) 2cdv 1.8 monomer Cytochrome C5 (Azotobacter vinelandii) 1cc5 2.5 monomer Cytochrome C550 (Paracoccus denitrificans) 155c 2.5 monomer; some UNK residues at C terminus Cytochrome C551 (Pseudomonas aeruginosa) 351c 1.6 monomer; oxidized 451c 1.6 monomer; reduced Cytochrome P450CAM (Camphor Monooxygenase) (Pseudomonas putida) 2cpp 1.63 monomer; with bound camphor 3cpp 1.9 monomer; with reduced camphor & CO 4cpp 2.11 monomer; with adamantane 5cpp 2.08 monomer; with adamantane 6cpp 1.9 monomer; with camphane 7cpp 2.0 monomer; with norcamphor 8cpp 2.1 monomer; with thiocamphor Cytotoxic T-Lymphocyte Proteinase I (Mus musculus) 2cp1 --- non-experimental model Deoxyribonucleic Acid (DNA) 1ana 2.1 tetramer 1bd1 1bna 1d10 1d11 1d12 1d13 1d14 1d15 1d16 1d17 1d18 1d19 1d20 1d21 1d22 1dcg 1dn4 1dn5 1dn6 1dn7 1dn8 1dn9 1dne 1dnf 1dnh 1dnm 1dnn 1dns 1zna 2ana 2bna 2dcg 2dnd 2.2 complex with distamycin 2zna 3ana 3bna 3dnb 3zna 4bna 4dnb 5ana 5bna Dihydrofolate reductase (Escherichia coli) 4dfr 1.7 monomer - 2 independent chains given; chain B preferred for structural comparisons; resistant strain; complex with methotrexate 4dfrw half of coords eliminated; monomer remains 5dfr 2.3 monomer; apo; resistant strain 6dfr 2.4 monomer; complex with NADP+; resistant strain 7dfr 2.5 monomer; complex with folate & NADP+; resistant strain Dihydrofolate reductase (Gallus gallus) 8dfr 1.7 monomer Dihydrofolate reductase (Homo sapiens) 1dhf 2.3 monomer - 2 chains given; complex with folate; chain B preferred 1dhfw chain B; half of coords eliminated; monomer remains 2dhf 2.3 monomer; complex with 5-deazafolate Dihydrofolate reductase (Lactobacillus casei) 3dfr 1.7 monomer; complex with NADPH & methotrexate DNA Polymerase I Klenow Fragment (Escherichia coli) 1dpi 2.8 CA Eco R1 Endonuclease (Escherichia coli) 1r1e 2.7 CA dimer (a2) - 1 chain given; complex with DNA Eglin C (Hirudo medicinalis) DUP1cse 1.2 monomer; complex with subtilisin; duplicate listing DUP1tec 2.2 monomer; complex with thermitase; duplicate listing Elastase, Human Neutrophil (Homo sapiens) 1hne 1.84 monomer; complex with inhibitor - Methoxysuccinyl-Ala- Ala-Pro-Ala-Chloromethyl ketone Elastase (Sus Scrofa) 1est 2.5 monomer; tosyl 2est 2.5 monomer; complex with trifluoro-L-lysyl-L-alanyl- P-trifluoromethyl-phenylanilide 3est 1.65 monomer; native Elongation Factor TU (Escherichia coli B) 1efm 2.7 CA trypsin modified; excised residues labeled EXC 1etu 2.9 monomer; domain I (part of molecule not included in data set); complex with guanosine diphosphate; excised residues labeled EXC Enolase (2-Phospho-D-Glycerate Hydrolase) (Saccharomyces cerevisiae) 2enl 2.25CA dimer (a2) - 1 chain given Erabutoxin (Laticauda semifasciata) 1nxb 1.38 monomer; "B"; differs from 5ebx by one residue; inverted pair - res 6 and 7 differ from 5ebx and 3ebx 3ebx 1.4 monomer; B; differs from 5ebx by one residue 5ebx 2.0 monomer; A; differs from 3ebx by one residue Ferredoxin (Azotobacter vinelandii) 4fd1 1.9 monomer; supersedes 3fd1 1fd2 1.9 monomer; mutant C20A 2fd2 1.9 monomer; mutant C24A Ferredoxin (Bacillus thermoproteolyticus) 1fxb 2.0 monomer 2fxb 2.3 monomer; supersedes 1fxb Ferredoxin (Peptococcus aerogenes) 1fdx 2.0 monomer Ferredoxin (Spirulina platensis) 3fxc 2.5 monomer Ferredoxin NADP+ Oxidoreductase (Spinacia oleracea) 1fnr 2.2 monomer? 2fnr 3.0 monomer?; complex with 2'phospho 5' AMP FK506 Binding Protein (Homo sapiens) 1fkf 1.7 monomer; complex with FK506 immunosuppressant Flavocytochrome B2 (Saccharomyces cerevisiae) 1fcb 2.4 dimer? - 2 chains given; looks better as tetramer Flavodoxin (Clostridium MP) 3fxn 1.9 monomer; oxidized form 4fxn 1.8 monomer; semiquinone form Flavodoxin (Desulfovibrio vulgaris) 1fx1 2.0 monomer D-Galactose/D-Glucose Binding Protein (Escherichia coli B/R) 1gbp 3.0 CA all residues UNK 2gbp 1.9 monomer complex with beta-D-glucose and Ca++ 3gbp 2.4 monomer complex with glucose and Ca++; supersedes 1gbp Gene 5 DNA Binding Protein (Filamentous bacteriophage FD M13) 2gn5 2.3 dimer (a2) - 1 chain given 2gn5w made; checked with Insight; structures same as lit Glucagon (Sus scrofa) related to insulin and avian pancreatic peptide 1gcn 3.0 trimer in crystal (a3) - 1 chain given; monomer in solution; high temperature factors; presumed to be in crystaline configuration on the receptor 1gcnw made; checked D-Glucose 6-Phosphate Isomerase (Sus scrofa) 1pgi 3.5 CA dimer (a2) - 1 chain given; all residues UNK Glutamine Synthase (Salmonella typhimurium) 2gls 3.5 dodecamer (a12) - 12 chains given; includes Mn++ and water Glutathione Peroxidase (Bos taurus) 1gp1 2.0 tetramer (a4) - 2 chains given 1gp1 matrix as given in Intl Tables doesn't work -- subunits too far apart; Insight's matrix doesn't work either -- there is some overlap in the top two subunits and the bottom two are too far apart -- the molecule is not compact as in the lit; modified matrices don't seem to work either. Glutathione Reductase (Homo sapiens) 3grs 1.54 dimer (a2) - 1 chain given; oxidized; supersedes 2grs; 3grsw 3grs.mtx; made; checked on Iris; Insight can't find space group B 2 D-Glyceraldehyde-3-Phosphate Dehydrogenase (Bacillus Stearothermophilus) 1gd1 1.8 tetramer (a4) - 4 chains given; holo 2gd1 2.5 tetramer (a4) - 4 chains given; apo D-Glyceraldehyde-3-Phosphate Dehydrogenase (Homarus americanus) 1gpd 2.9 tetramer (a4) - 2 chains given; complex with NAD & phosphates 1gpdw made 4gpd 2.8 tetramer (a4) - 4 chains given; apo; supersedes 2gpd D-Glyceraldehyde-3-Phosphate Dehydrogenase (Homo sapiens) 3gpd 3.5 tetramer (a4) - 2 chains given; complex with NAD & phosphates; 3gpdw made; checked Glycolate Oxidase (Spinacia oleracea) 1gox 2.0 octamer (a8) or tetramer (a4) (equil.) - 1 chain given 1goxw made; checked Gramicidin A (Bacillus brevis) 1gma 0.86 dimer (a2) - 2 chains given; several amino acids are in D config Hannuka Factor (Homo sapiens) 1hf1 --- model Heat Shock Cognate Protein (Bos taurus) 1hsc 2.2 CA N-terminal fragment Hemagglutinin (Influenza virus, 1968 X.31 strain) bromelain digested (missing hydrophobic anchor) 1hmg 3.0 trimer of dimers (3[ab]) - 6 chains given; G146D mutant 2hmg 3.0 trimer of dimers (3[ab]) - 6 chains given; G146D mutant 3hmg 2.9 trimer of dimers (3[ab]) - 6 chains given; L226Q mutant 4hmg 3.0 trimer of dimers (3[ab]) - 6 chains given; L226Q mutant; complex with sialic acid 5hmg 3.2 trimer of dimers (3[ab]) - 6 chains given; D112G (HA2) mutant; complex with sialic acid Hemerythrin (Siphonosoma species) 1hr3 5.5 CA trimer (a3?) - 3 chains given; all residues UNK Hemerythrin (Themiste dyscritum) 1hmq 2.0 octamer (a8) - 4 chains given; two chains each from two different octamers; met 1hmqw made; checked with Insight -- seems to be the same as the one it makes, but has big holes; checked both ways; re-ordered literature 1hmz 2.0 octamer (a8) - 4 chains given; azidomet Hemerythrin B (Phascolopsis gouldii) 1hrb 5.5 CA monomer Hemoglobin (Equus caballus) 2dhb 2.8 tetramer (a2b2) - 2 chains given; deoxy; supersedes 1dhb 2dhbw made; checked; looks ok on Iris, but Insight can't make similar molecule 2mhb 2.0 tetramer (a2b2) - 2 chains given; aquo met Hemoglobin (Homo sapiens) 1coh 2.9 tetramer (a2b2) - 4 chains given; alpha-ferrous-carbonmonoxy; beta-cobaltous-deoxy; T state 1hco 2.7 tetramer (a2b2) - 2 chains given; carbonmonoxy 2hco 2.7 tetramer (a2b2) - 2 chains given; carbonmonoxy; energy minimized 2hhb 1.74 tetramer (a2b2) - 4 chains given; deoxy; "best estimate of coordinates" 3hhb 1.74 tetramer (a2b2) - 2 chains given; deoxy; "symmetry averaged" 4hhb 1.74 tetramer (a2b2) - 4 chains given; deoxy; "unrestrained refinement" 1hho 2.1 tetramer (a2b2) - 2 chains given; A; oxy Hemoglobin F (Fetal) (Homo sapiens) 39/146 residues of subunit G are different from subunit B of H. sapiens adult; other subunit is the same 1fdh 2.5 tetramer (a2b2) - 2 chains given; deoxy 1fdhw made; checked Hemoglobin S (Sickle Cell) (Homo sapiens) 1hbs 3.0 tetramer (a2b2) - 8 chains given; deoxy; differs from Hemoglobin A by one residue; would be useful to include region around point mutation in predictions 1hbsw half of records eliminated; only need 4 subunits, not 8 Hemoglobin S (Sickle Cell) (Odocoileus virginianus) 1hds 1.98 tetramer (a2b2) - 4 chains given Hemoglobin (Scapharca inaequivalvis) 1sdh 2.4 dimer - 2 chains given; carbonmonoxy 2sdh 2.4 dimer - 2 chains given; deoxy Hemoglobin III (Erythrocruorin) (Chironomous Thummi Thummi) 1eca 1.4 monomer; aquo met 1ecd 1.4 monomer; deoxy 1ecn 1.4 monomer; cyano met 1eco 1.4 monomer; carbon monoxy Hemoglobin V (Petromyzon marinus) 2lhb 2.0 monomer or dimer - 1 chain given; cyano, met; hydrogen atoms added by computer Hexokinase A (Saccharomyces cerevisiae) 1hkg 3.5 monomer; complex with glucose; many UNK residues Hexokinase B (Saccharomyces cerevisiae) 2yhx 2.1 probably multimer - 1 chain given; complex with orthotoluoylglucosamine; many residues UNK High Potential Iron Protein (HIPIP) (Chromatium vinosum, strain D) 1hip 2.0 monomer Hirudin (Hirudo medicinalis) 2hir NMR monomer; wt; multiple solutions 4hir NMR monomer; K47E mutant; multiple solutions 5hir NMR monomer; energy-minimized average structure 6hir NMR monomer; K47E mutant; energy-minimized average structure HIV-1 Protease (HIV I) 1hvp --- model; complex with substrate; non-experimental 2hvp 3.0 CA dimer (a2) - 1 chain given 3hvp 2.8 dimer (a2) - 1 chain given; 2 Cys residues replaced by ABA 3hvpw made; looks ok 4hvp 2.3 dimer (a2) - 2 chains given; complex with inhibitor; 2 Cys residues replaced by ABA Human Class I Histocompatibility Antigen A2 (Homo sapiens) 1hla 3.5 CA dimer (ab) - 2 chains given Human Class I Histocompatibility Antigen A2.1 (Homo sapiens) 3hla 2.6 dimer (ab) - 2 chains given Human Class I Histocompatibility Antigen AW 68.1 (Homo sapiens) membrane anchor cleaved off with papain 2hla 2.6 dimer (ab) - 2 chains given Hyaluronic Acid (synthetic & Homo sapiens) 1hya 3.0 NOT PROTEIN 2hya 3.0 NOT PROTEIN 3hya 3.0 NOT PROTEIN 4hya 3.0 NOT PROTEIN P-Hydroxybenzoate Hydroxylase (Pseudomonas fluorescens) 1phh 2.3 dimer (a2) - 1 chain given; complex with FAD & DHB 1phhw made; no picture of dimer in lit, but same as one of molecules made by Insight 2phh 2.7 dimer (a2) - 1 chain given; complex with PHBH & ADPR Immunoglobulin IgA Fab Fragment Hy/Hel-10 (Mus musculus) 1hfm --- non-experimental 2hfm --- non-experimental Immumoglobulin IgA FV Fragment Anti-Alpha1->6 Dextran 19.1.2 (Mus musculus) 1fvb --- non-experimental 2fvb --- non-experimental; energy minimized model Immunoglobulin IgA FV Fragment Anti-Alpha 1->6 Dextran W3129 (Mus musculus) 1fvw --- non-experimental 2fvw --- non-experimental; energy minimized model Immunoglobulin IgA(Kappa) Fab Fragment McPC603 (Mus musculus) 1mcp 2.7 H & L chains; Insight makes a trimer of dimers, which looks like the basic crystallographic unit; re-ordered literature 2mcp 3.1 H & L chains; complex with phosphocholine Immunoglobulin IgA(Kappa) Fab Fragment J539 (Mus musculus) 1fbj 2.6 H & L chains 2fbj 1.95 H & L chains; supersedes 1fbj Immunoglobulin IgG1 Fab Fragment (Homo sapiens) 2fb4 1.9 H & L chains; H chain is truncated from 2ig2; some very close crystal contacts 2ig2 3.0 H & L chains; some of sequence & conformation is taken from 1fc1 Immunoglobulin IgG1(Kappa) Fab Fragment Hy/Hel-10 (Mus musculus & Gallus gallus) 3hfm 3.0 three chains (abx) - 2 Fab & lysozyme; similar to 2hfl, not identical Immunoglobulin IgG1 Fab Fragment Hy/Hel-5 (Mus musculus) 2hfl 2.54 three chains (abx) - 2 Fab & lysozyme Immunoglobulin IgG2a(Kappa) Fab Fragment (Mus musculus) 4fab 2.7 H & L chains; complex with fluorescein (antigen) Immunoglobulin IgG2b(Kappa) Fab R19.9 (Mus musculus) 1f19 2.8 H & L chains; similar to 3hfm Immunoglobulin IgG(Lambda) Fab New (Homo sapiens) 3fab 2.0 H & L chains; similar to 3hfm Immunoglobulin Fab Heterologous Light Chain Dimer (Homo sapiens) 1mcw 3.5 dimer (ab) - 2 chains given; hybrid of Weir (H analog) & MCG (L analog); chimera Immunoglobulin Fab Bence/Jones Protein (Homo sapiens) 2rhe 1.6 dimer (a2) - 1 chain given; lambda; variable domain 2rhew made; checked Immunoglobulin Lambda Light Chain Dimer (Homo sapiens) 1mcg 2.3 CA dimer (a2) - 2 chains given 2mcg 2.0 dimer (a2) - 2 chains given; trigonal form (deionized water); supersedes 1mcg 3mcg 2.0 dimer (a2) - 2 chains given; orthorhombic form (ammonium sulfate - high salt) Immunoglobulin IgG(Kappa) Fab Bence/Jones REI (Homo sapiens) 1rei 2.0 dimer (a2) - 2 chains given; variable portion of protein Immunoglobulin IgG1 Fc Fragment (Homo sapiens) 1fc1 2.9 dimer (a2) - 2 chains given (a2) 1fc2 2.8 dimer (a2) - 2 chains given (a + s); half of Ig given; complex with Fragment B of Protein A 1fc2w dimerized acc to included matrix; checked; missing piece is due to assymetry of protein fragment; original lit checked; protein fragment at elbow in chains Immunoglobulin IgG1 pFc' Fragment (Cavia porcellus) 1pfc 3.125 dimer (a2) - 1 chain given 1pfcw made; checked Immunoglobulin IgE Fc' Fragment (Homo sapiens) 1ige --- model; should NOT be used Insulin (Bos taurus) Insulin is produced & stored as a hexamer of dimers, but it is active as a dimer. Subunit B is the same as S. scrofa. 2ins 2.5 dodecamer (6ab) - 4 chains given; Des-Phe B1 Insulin (Sus scrofa) Insulin is produced & stored as a hexamer of dimers, but it is active as a dimer. Subunit B is the same as B. taurus. 1ins 1.5 dodecamer (6ab) - 4 chains given 3ins 1.5 dodecamer - 4 chains given; joint x-ray & neutron scattering; 2-Zn; has hydrogens 4ins 1.5 dodecamer - 4 chains given; supersedes 1ins Insulin-like Growth Factor (Somatomedin) (Homo sapiens) 1gf1 --- I; non-experimental; should NOT be used 1gf2 --- II; non-experimental; should NOT be used Interleukin-1 Beta (Homo sapiens) different structures done by different groups 1i1b 2.0 monomer 2i1b 2.0 monomer 4i1b 2.0 monomer Interleukin-8 Beta (Homo sapiens) 1il8 NMR dimer; energy minimized average structure 2il8 NMR dimer; 41 simulated annealing structures Iota Carrageenan (Rhodophycae) 1car 3.0 polysaccharide; NOT PROTEIN Isocitrate Dehydrogenase (Escherichia coli) 3icd 2.5 dimer - 1 chain given 3icdw made; checked 4icd 2.5 dimer - 1 chain given; phosphorylated Kallikrein A (Sus scrofa) related to tonin 2kai 2.5 complex with BPTI; chain cleaved - separate identifiers 2pka 2.05 chain cleaved - separate identifiers; 4 chains given; 2 chains should be removed before processing 2pkaw half of coords eliminated; monomer remains; checked Keratan Sulfate (Bos taurus) 1kes 3.0 polysaccharide; NOT PROTEIN 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase (Pseudomona putida) 1kga 3.5 CA trimer - 1 chain given; all residues UNK L7/L12 50S Ribosomal Protein - C Terminal Domain (Escherichia coli, MRE 600) 1ctf 1.7 "monomer" - whole protein is a dimer, but N terminus is thought to be required; fragment of protein Alpha Lactalbumin (Papio cynocephalus) 1alc 1.7 monomer; sequence deduced from x-ray Beta Lactamase (Bacillus lichenformis 749/C) 2blm 2.0 CA monomer; 2 chains given Beta Lactamase (Staphylococcus aureus pc1) 1blm 2.5 CA 3blm 2.0 monomer?; supersedes 1blm; check lit *********************************************************** All lactate dehydrogenases are probably tetramers, but they seem to crystallize in unusual space groups, or else they don't follow the crystallographic symmetry.I can't get Insight to make a molecule that seems reasonable to me. *********************************************************** L-Lactate Dehydrogenase (Bacillus stearothermophilus) 1ldb 2.8 tetramer (a4) - 1 chain given; apo 1ldbw made from matrices given; checked; no picture in lit of tetramer 2ldb 3.0 tetramer (a4) - 1 chain given; complex with NAD & F1,6P L-Lactate Dehydrogenase (Lactobacillus casei) 1llc 3.0 tetramer (a4) - 1 chain given; complex with CO2 & F1,6P 1llcw made from matrices given; checked; no picture from original lit - difficulty getting literature cited Lactate Dehydrogenase (Mus musculus) 2ldx 2.96 tetramer (a4) - 1 chain given; isoenzyme C4; apo; supersedes 1ldx 2ldxw made; looks ok on screen, but doesn't look like lit Lactate Dehydrogenase (Squallus acanthias) 3ldh 3.0 tetramer (a4) - 1 chain given; M4; complex with NAD & pyruvate 6ldh 2.0 tetramer (a4) - 1 chain given; M4; apo 6ldhw made; looks different from 1llc; I checked this by changing the non-standard space group F 4 2 2 to I 4 2 2, which uses the right-handed coordinate system. Four of the replicates used by Insight to create the tetramer are the same as those mentioned in the MTRIX records. 8ldh 2.8 tetramer (a4) - 1 chain given; M4; apo; complex with citrate 1ldm 2.1 tetramer (a4) - 1 chain given; M4; complex with NAD & oxamate Lactate Dehydrogenase (Sus scrofa) 5ldh 2.7 tetramer (a4) - 1 chain given; H4; complex with NAD & S-Lac Lambda Repressor (Phage lambda) 1lrd 2.5 dimer (a2) - 2 chains given + dsDNA; repressor-operator complex 1lrp 3.2 CA dimer (a2) - 1 chain given; N-terminal domain Lectin (Pisum sativum) 2ltn 1.7 tetramer (a2b2) - 4 chains given Leghemoglobin (Lupinus luteus l) For these entries, the 1s & 2s of a pair were refined in diff. manners. 1lh1 2.0 monomer; acetate, met 2lh1 2.0 monomer; acetate, met 1lh2 2.0 monomer; aquo, met 2lh2 2.0 monomer; aquo, met 1lh3 2.0 monomer; cyano, met 2lh3 2.0 monomer; cyano, met 1lh4 2.0 monomer; deoxy 2lh4 2.0 monomer; deoxy 1lh5 2.0 monomer; fluoro, met 2lh5 2.0 monomer; fluoro, met 1lh6 2.0 monomer; nicotinate, met 2lh6 2.0 monomer; nicotinate, met 1lh7 2.0 monomer; nitrosobenzene 2lh7 2.0 monomer; nitrosobenzene Leucine Binding Protein (Escherichia coli, strain K12) 2lbp 2.4 monomer; similar to 2liv Leucine/Isoleucine/Valine Binding Protein (Escherichia coli) 2liv 2.4 monomer; similar to 2lbp Lysozyme (Gallus Gallus) 1lym 2.5 monomer - 2 chains given 2lym 2.0 monomer; 1 atm; 1.4 M NaCl 3lym 2.0 monomer; 1000 atm; 1.4 M NaCl 1lyz 2.0 monomer; unrefined coordinates 2lyz 2.0 monomer; after refinement 1 3lyz 2.0 monomer; different refinement 4lyz 2.0 monomer; different refinement 5lyz 2.0 monomer; different refinement 6lyz 2.0 monomer; different refinement 7lyz 2.5 monomer; triclinic 8lyz 2.5 monomer; iodine inactivated 9lyz 2.5 substrate only 1lzh 6.0 CA monoclinic 2lzh 6.0 CA orthorhombic 1lzt 1.97 monomer; diff refinement from 2lzt 2lzt 1.97 monomer; diff refinement from 1lzt Lysozyme (Homo sapiens) 1lz1 1.5 monomer Lysozyme (Meleagris gallopavo) 1lz2 2.8 CA similar to Gallus, but not identical 2lz2 2.2 monomer; difficulty obtaining original literature Lysozyme (Phage T4 in Escherichia coli) 1lyd 2.0 monomer; synthetic coding 2lzm 1.7 monomer; supersedes 1lzm 3lzm 1.7 monomer; same as 2lzm, but better refinement use as basis for comparison of 1lxx mutants 1l01 - 1l35 mutants of T4 lysozyme Cytoplasmic Malate Dehydrogenase (Sus scrofa) 4mdh 2.5 dimer (a2) - 2 chains given; supersedes 2mdh Melittin (Apis mellifera) 1mlt 2.0 tetramer (a4) - 2 chains given 2mlt 2.0 tetramer (a4) - 2 chains given; supersedes 1mlt 2mltw made; Insight (not Intl Tables) matrix; checked; looks ok Mengo Encephalomyocarditis Virus Coat Protein (Mengo virus) 2mev 3.0 240mer - 4 chains given; supersedes 1mev CD-7 Metallothionein-2 (Homo sapiens) Alpha: one residue differs from Oryctolagus; 2 from Rattus Beta: several differences 1mhu NMR alpha domain; 31 residues long 2mhu NMR beta domain; 30 residues long CD-7 Metallothionein-2 (Oryctolagus cuniculus) Alpha: one residue differs from Homo sapiens; 2 from Rattus Beta: several differences 1mrb NMR alpha domain; 31 residues long 2mrb NMR beta domain; 30 residues long CD-7 Metallothionein-2 (Rattus rattus) Alpha: two residues differ each from Homo sapiens and from Oryctolagus. Beta: several differences 1mrt NMR alpha domain; 31 residues long 2mrt NMR beta domain; 30 residues long Monellin (Dioscoreophyllum cumminsii Diels) 1mon 2.75 CA heterodimer - 8 chains given Muconolactone Isomerase (Pseudomonas putida) 1mli 3.3 CA decamer - 1 chain given Murein Lipoproten (Escherichia coli) mmlp --- non-experimental Myoglobin (Aplysia limacina) 1mba 1.6 monomer; met 2mba 2.0 monomer; azide 3mba 2.0 monomer; fluoride 4mba 2.0 monomer; imidazole Myoglobin (Phoca vitulina) 1mbs 2.5 monomer; similar to Physeter; Insight can't match space group A 2 Myoglobin (Physeter catodon) 1mb5 1.8 monomer; carbonmonoxy; neutron study; has hydrogens 1mbc 1.5 monomer; FeII; carbonmonoxy; 260K 1mbd 1.4 monomer; deoxy; pH 8.4 1mbn 2.0 monomer; ferric; met 4mbn 2.0 monomer; met; supersedes 2mbn 5mbn 2.0 monomer; deoxy; supersedes 3mbn 1mbo 1.6 monomer; oxy; pH 8.4 1mbw 1.9 monomer; met; X0M & D122N mutant Myoglobin (Sus scrofa) 1pmb 2.5 monomer - 2 chains given; aquo met 1pmbw half of coords eliminated; monomer remains Myohemerythrin (Themiste zostericola) 2mhr 1.7/1.3 monomer; has hydrogens Oncomodulin (Rattus norvegicus) 1omd 1.85 monomer? Ovomucoid Third Domain (Coturnix coturnix japonica) similar to Lophura, but not identical 1ovo 1.9 monomer, but crystallographically an octamer (a8) - 4 chains given; part of protein 1ovow made; checked -- It really looks like two tetramers - ABGH and CDEF. N.B. C and D in the 1ovow file are NOT the same CD as in the 1ovo file!! Ovomucoid Third Domain (Lophura nycthemera) similar to Coturnix, but not identical 2ovo 1.5 monomer - 1 chain given; part of protein 1-Beta-Mercaptopropionate Oxytocin (synthetic) 1xy1 1.04 monomer - 2 chains given; 8 residues; wet form; has H's 1xy2 1.20 monomer - 2 chains given; 8 residues; dry form; has H's Avian Pancreatic Polypeptide (Meleagris gallopavo) related to insulin and glucagon 1ppt 1.37 dimer (a2) - 1 chain given 1pptw made; checked; ok Papain (Carica papaya) 1pad 2.8 monomer; derivative of C25; based on 8pap 2pad 2.8 monomer; derivative of C25; based on 8pap; supersedes 3pap 4pad 2.8 monomer; derivative; based on 8pap; supersedes 5pap 5pad 2.8 monomer; derivative; based on 8pap; supersedes 6pap 6pad 2.8 monomer; derivative; based on 8pap; supersedes 7pap 9pap 1.65 monomer; supersedes 8pap; Cys-25 oxidized 1ppd 2.0 monomer; 2-Hydroxyethylthiopapain; C25 inhibited Pepsin (Sus scrofa) Sequence is the same as pepsinogen, minus the leader peptide. 3pep 2.3 monomer 4pep 1.8 monomer; supersedes 1pep 5pep 2.34 monomer; supersedes 2pep Pepsinogen (Sus scrofa) Sequence is the same as pepsin, plus the leader peptide. 1psg 1.65 monomer; propeptide residues labelled 1P - 44P; may be dimer in crystal; difficulty obtaining original literature Phaseolin (Phaseolus vulgaris) 1phs 3.0 CA dodecamer? - 3 chains given; crystallizes as tetramer of trimers Phosphofructokinase (Bacillus stearothermophilus) 3pfk 2.4 tetramer (a4) - 1 chain given; unliganded 3pfkw made; checked; looks ok 4pfk 2.4 tetramer (a4) - 1 chain given; complex with F6P and ADP/Mg++ 5pfk 7.0 CA complex with inhibitor Phosphofructokinase (Escherichia coli) 1pfk 2.4 tetramer (a4) - 2 chains given; complex with F1,6P and ADP/Mg++ 2pfk 2.4 tetramer (a4) - 4 chains given, but 2 are part of one tetramer & the other two are part of another; unliganded 2pfkw made; checked Phosphoglycerate Kinase (Equus caballus) 2pgk 3.0 all residues UNK Phosphoglycerate Kinase (Saccharomyces cerevisiae) 3pgk 2.5 monomer; complex with ATP, Mg++, and 3-Phosphoglycerate; some crystal contacts are very close; contacts between molecules are as close as contacts between domains Phosphoglycerate Mutase (Saccharomyces cerevisiae) 3pgm 2.8 tetramer (a4) - 1 chain given 3pgmw made; checked Phospholipase A2 (Bos taurus l.) 1bp2 1.7 monomer 3bp2 2.1 transaminated Pro-Phospholipase A2 (Bos taurus l.) 2bp2 3.0 monomer; zymogen, with 7 res leader; coordinates for the leader peptide are not included Phospholipase A2 (Crotalus atrox) 1pp2 2.5 dimer (a2) - 2 chains given Phospholipase A2 (Sus Scrofa) 1p2p 2.6 monomer 3p2p 2.1 mutant; surface loop deleted Photoactive Yellow Protein (Ectothiorhodospira halophila) 1phy 2.4 CA Photosynthetic Reaction Center (Rhodopseudomonas viridis) 1prc 2.3 tetramer (abcd) - 4 chains given; membrane protein - solvent accessibility info will need to be re-interpreted Plastocyanin (Populus nigra variant italica) 1pcy 1.6 monomer; Cu++; pH 6.0 2pcy 1.8 monomer; apo; pH 6.0 3pcy 1.9 monomer; Hg++ 4pcy 2.15 monomer; crosslinked 5pcy 1.80 monomer; Cu+; pH 7.0 6pcy 1.90 monomer; Cu+; pH 3.8 Plastocyanin (Enteromorpha prolifera) 7pcy 1.8 monomer; hydrogens included Poliovirus, Type I, Mahoney Strain (Homo sapiens) 2plv 2.88 240mer - 4 chains given Prealbumin (Homo sapiens) 2pab 1.8 tetramer (a4) - 2 chains given 2pabw made acc. to file; checked Proteinase A (Streptomyces griseus, strain K1) 2sga 1.5 monomer; sequence numbered as chymotrypsinogen - gaps; lots of crystal contacts; phe sticking out; see MD paper by Avbelj et al., Biochemistry 29 (1990) 1sgc 1.8 complex with chymostatin; seq numbers as for 2sga Proteinase B (Streptomyces griseus, strain K1) 3sgb 1.8 monomer; complex with ovomucoid inhibitor; numbering has gaps 4sgb 2.1 monomer; complex with potato inhibitor; inhibitor is 51 res long -- could be used, too Proteinase K (Tritirachium album limber) 2prk 1.5 monomer; pseudodimer in crystal Proteinase Inhibitor IIA (Bos taurus) 1bus NMR monomer - 5 chains given 2bus NMR monomer - 1 chain given -- energy minimized structure Pseudoazurin (Alcaligenes faecalis, strain S-6) 1paz 1.55 monomer; oxidized Cu++ at pH 6.8 2paz 2.0 monomer Inorganic Pyrophosphatase (Saccharomyces cerevisiae) 1pyp 3.0 dimer (a2) - 1 chain given 1pypw dimerized acc to included matrix; looks ok; diff from dimer Insight makes -- non-crystallographic symmetry Pyruvate Kinase (Felis domestica) 1pyk 2.6 CA all residues UNK C-H-RAS P21 Protein Catalytic Domain (Homo sapiens) 2p21 2.2 CA 3p21 2.2 CA mutant (G12V) Rat Mast Cell Protease II (Rattus rattus) 3rp2 1.9 monomer - 2 chains given; residue numbering based on chymotrypsin -> gaps; 3rp2w made; checked Relaxin (Sus scrofa) 1rlx --- non-experimental; based on insulin 2rlx --- non-experimental 3rlx --- non-experimental 4rlx --- non-experimental Retinol Binding Protein (Homo sapiens) 1rbp 2.0 monomer? Rhinovirus 14 Coat Protein (Homo sapiens) Icosohedral - 240mer; 4 chains given = 1 unit of icosohedron 1r08 3.0 complex with antiviral agent 1rmu 3.0 mutant of 1r08; otherwise same 2r04 3.0 supersedes 1r04; complex with antiviral agent (WIN IV); 2r06 3.0 supersedes 1r06; complex with antiviral agent (WIN VI); 2r07 3.0 supersedes 1r07; complex with antiviral agent (WIN VII); 2rm2 3.0 supersedes 1rm2; complex with antiviral agent (WIN II); 2rmu 3.0 mutant (V188L in chain 1); icosohedral; 2rr1 3.0 supersedes 1rr1; complex with antiviral agent (WIN I[R]) 2rs1 3.0 supersedes 1rs1; complex with antiviral agent (WIN I[S]); 2rs3 3.0 supersedes 1rs3; complex with antiviral agent (WIN III[S]); 2rs5 3.0 supersedes 1rs5; complex with antiviral agent (WIN V[S]); 4rhv 3.0 Rhinovirus Serotype 1A Coat Protein (Homo sapiens) Icosohedral - 240mer; 4 chains given = 1 unit of icosohedron 1r1a 3.2 Rhodanese (Bos taurus) 1rhd 2.5 monomer Ribonuclease A (Bos taurus) 1rbb 2.5 B; 2 identical chains given 1rn3 1.45 monomer 1rns 2.0 S; single chain of 1rn3 split into 2 chains 5rsa 2.0 monomer; joint x-ray & neutron - contains hydrogens 6rsa 2.0 monomer; complex with uridine vanadate; joint x-ray & neutron 7rsa 1.26 monomer; phosphate-free; joint x-ray & neutron 1rsm 2.0 monomer; cross-linked 1srn 1.8 dimer - 2 chains given; semi-synthethic - chains are portions of RNase A Ribonuclease T1 (Aspergillus oryzae) 1rnt 1.9 monomer; complex with 2'guanylic acid 2rnt 1.8 monomer; complex with guanyl-2'6'-guanosine 3rnt 1.8 monomer; complex with vanadate Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RUBISCO) (Rhodospirillum rubrum) 2rub 1.7 CA dimer - 2 chains given Rous Sarcoma Virus Protease (Rous Sarcoma virus, strain PR-C) 2rsp 2.0 dimer (a2) - 2 chains given Rubredoxin (Clostridium pasteurianum) 4rxn 1.2 monomer; oxidized; unconstrained; supersedes 2rxn 5rxn 1.2 monomer; oxidized; constrained; supersedes 2rxn Rubredoxin (Desulfovibrio desulfuricans, strain 27774) 6rxn 1.5 monomer Rubredoxin (Desulfovibrio gigas) 1rdg 1.4 monomer; oxidized Rubredoxin (Desulfovibrio vulgaris) 3rxn 1.5 monomer 7rxn 1.5 monomer; supersedes 3rxn; Fe+++ and sulfate Sarcoplasmic Calcium-Binding Protein (Nereis diversicolor) 1scp 3.0 CA monomer - 2 chains given Satellite Tobacco Necrosis Virus (STNV) 2stv 2.5 60mer - 1 chain given Scorpion Neurotoxin Variant 3 (Centruroides sculpturatus Ewing) 1sn3 1.8 monomer Southern Bean Mosaic Virus Coat Protein (SBMV) 4sbv 2.8 540mer - 3 chains given; supersedes 3sbv Staphylococcyl Nuclease (Staphylococcus aureus) 1snc 1.65 monomer; complex with Ca++ & inhibitor 1snm 1.74 monomer; E43D mutant; complex with Ca++ & deoxythymidine 3'5'bisphosphate 2sns 1.5 monomer; complex with 2'deoxy 3'5' diphosphothymidine; Streptomyces Subtilisin Inhibitor (Streptomyces albogriseolus, S-3253) 2ssi 2.6 dimer (a2) - 1 chain given; supersedes 1ssi 2ssiw made; checked Subtilisin BPN (Novo) (Bacillus amyloliquefaciens) sequence very similar to Subtilisin Carlsberg 1sbt 2.5 monomer 2sbt 2.8 monomer 1sic 2.0 CA BPN'; complex with inhibitor; inhibitor is a dimer & binds 2 subtilisins - 1 chain of each given 1st2 2.0 BPN'; peroxide inactivated (Mets oxidized) 2st1 1.8 BPN' 1s01 1.7 monomer; mutant (M50F, N76D, G169A, Q206C, Y217K, & N218S); residue 206 may be persulfide 2sni 2.1 complex with chymotrypsin inhibitor (Hordeum vulgare) Subtilisin Carlsberg (Bacillus subtilis) sequence very similar to Subtilisin BPN (Novo) 1cse 1.2 monomer; complex with Eglin-C (Hirudo medicinalis) 1sbc 2.5 monomer 2sec 1.8 complex with N-Acetyl-Eglin-C (Hirudo medicinalis) Cu, Zn Superoxide Dismutase (Bos taurus) 2sod 2.0 dimer (a2) - 4 chains given 2sodw made; checked Taka-Amylase A (Aspergillus oryzae) 2taa 3.0 monomer - 1 chain given Tendamistat (Streptomyces tendae) 2ait NMR monomer - 9 chains given; with hydrogens and hydrogen pseudoatoms; this file messes up in Insight 3ait NMR energy minimized model using AMBER 4ait NMR energy minimized model using FANTOM Thaumatin I (Thaumatococcus danielli Benth) 1thi 3.2 CA monomer Thermitase (Thermoactinomyces vulgaris) homologous to Subtilisin 1tec 2.2 monomer; complex with Eglin C (Hirudo medicinalis) (inhibitor) Thermolysin (Bacillus thermoproteolyticus) 3tln 1.6 monomer; supersedes 1tln & 2tln 4tln 2.3 monomer; complex with Leu-Hydroxylamine 5tln 2.3 monomer; complex with inhibitor 7tln 2.3 monomer; complex with inhibitor; supersedes 6tln 1tlp 2.3 monomer; complex with phosphoramidon 1tmn 1.9 monomer; complex with inhibitor 2tmn 1.6 monomer; complex with P-Leu 3tmn 1.7 monomer; complex with Val-Trp 4tmn 1.7 monomer; complex with CBZ-PHE-P-LEU-ALA 5tmn 1.6 monomer; complex with CBZ-PGL-LEU-LEU 6tmn 1.6 monomer; complex with CBZ-PGL-OLE-LEU 7tmn --- model of substrate GLY-TPH-LEU-LEU Thioredoxin (Escherichia coli B) 1srx 2.8 CA oxidized 1trx NMR monomer - 10 chains given; reduced Thymidine Phosphorylase (Escherichia coli K12) 1tpt 2.8 CA dimer - 1 chain given Tobacco Mosaic Virus (TMV vulgare strain) 2tmv 2.9 2130mer - 1 chain given; complex with RNA Tomato Bushy Stunt Virus (TBSV) 2tbv 2.9 180mer - 3 chains given Tonin (Rattus rattus) related to Kallikrein 1ton 1.8 monomer Transfer RNAs 1tn1 1tn2 1tra 2tra 3tra 4tra 4tna Triacylglycerol Acylhydrolase (Mucor miehei) 1tgl 1.9 CA monomer Triose Phosphate Isomerase (Gallus gallus) 1tim 2.5 dimer (a2) - 2 chains given Triose Phosphate Isomerase (Saccharomyces cerevisiae) 2ypi 2.5 dimer - 2 chains given; complex with PGA Tropomyosin (Oryctolagus cuniculus) 2tma 15.0 CA Troponin (Oryctolagus cuniculus) 1tnc --- non-experimental; based on parvalbumin Troponin C (Gallus gallus) Sequence similar to M. gallopavo (5 residues differ) 4tnc 2.0 monomer Troponin C (Meleagris gallopavo) Sequence similar to G. gallus (5 residues differ) 5tnc 2.0 monomer; supersedes 2tnc Trypsin Beta (Bos taurus) 1ntp 1.8 monomer; modified; monoisopropylphosphoryl inhibited; neutron data 1tld 1.5 monomer; beta; pH 5.3 1tpa 1.9 monomer; anhydro; complex with inhibitor 1tpo 1.7 monomer; beta; pH 5.0 1tpp 1.4 monomer; complex with APPA 2ptc 1.9 monomer; complex with PTI; supersedes 1ptc 2ptn 1.55 monomer; orthorhombic crystal; supersedes 1ptn; 2.4 M ammonium sulfate 3ptb 1.7 monomer; benzamidine inhibited; pH 7; supersedes 2ptb 3ptn 1.7 monomer; trigonal; 2.4 M ammonium sulfate 4ptp 1.34 monomer; diisopropylphosphoryl inhibited Trypsin (Rattus rattus) 1trm 2.3 monomer; 2 chains given; mutant (D102N); B chain more like native 1trmw made; checked 2trm 2.8 monomer; mutant (D102N); complex with benzamidine; pH 8 Trypsin (Streptomyces griseus, strain K1) 1sgt 1.7 monomer; sequence numbered as chymotrypsin - gaps Trypsin Inhibitor (Bos taurus) 4pti 1.5 monomer 5pti 1.0/1.8monomer; joint x-ray & neutron - H's & D's; crystal form II 6pti 1.7 monomer; crystal form III Trypsinogen (Bos taurus) 1tgb 1.8 monomer; CA form; trypsinogen; numbered acc. to chymotrypsin - gaps 1tgc 1.8 monomer; 50% methanol 50% water 1tgn 1.65 monomer 1tgs 1.8 monomer; complex with inhibitor 1tgt 1.7 monomer; 173 degrees K 2tga 1.8 monomer; 2.4 M MgSulfate 2tgd 2.1 monomer; complex with inhibitor 2tgp 1.9 monomer; complex with PTI 2tgt 1.7 monomer; 103 degrees K; 70:30 = methanol:water 2tpi 2.1 monomer; complex with PTI & Ile-Val; 2.4 MgSulfate 3tpi 1.9 monomer; complex with PTI & Ile-Val 4tpi 2.2 monomer; complex with PTI analog & Val-Val TRP Repressor (Escherichia coli) 1wrp 2.2 dimer (a2) - 1 chain given 2wrp 1.65 dimer (a2) - 1 chain given; apparent error in space group in PDB file - should be P 21 21 2 2wrpw made; checked 3wrp 1.8 dimer (a2) - 1 chain given; apo; apparent error in space group in PDB file - should be P 21 21 2 3wrpw made; checked Tryptophan Synthase (Salmonella typhimurium, strain TB2211/PSTH8) 1wsy 2.5 tetramer (a2b2) - 2 chains given 1wsyw made; checked Tumor Necrosis Factor Alpha (Homo sapiens) 1tnf 2.6 trimer (a3) - 3 chains given Tyrosyl-Transfer-RNA Synthetase (Bacillus stearothermophilus) 2ts1 2.3 dimer (a2) - 1 chain given; supersedes 1ts1 2ts1w made; checked 3ts1 2.7 dimer (a2) - 1 chain given; complex with tyrosinyl adenylate 4ts1 2.5 dimer (a2) - 1 chain given; complex with tyrosine; 318 - 417 deleted Ubiquitin (Homo sapiens) 1ubq 1.8 monomer Uteroglobin (Oryctolagus cuniculus) 1utg 1.34 dimer (a2) - 1 chain given; oxidized 1utgw made; checked 2utg 1.64 dimer (a2) - 2 chains given Wheat Germ Agglutinin (Triticum vulgaris) Two different isolectins; they differ by 5 amino acids. 3wga 1.8 dimer - 2 chains given; isolectin 2? 7wga 2.0 dimer - 2 chains given; isolectin 1 9wga 1.8 dimer - 2 chains given; supersedes 3wga; isolectin 2; this molecule does NOT look correct - too much empty space; orientation of different domains seems wrong. Made dimers by using each monomer and transforming acc to C2 matrix - 9wgaAC.pdb looks better and looks like one of dimers made by Insight. 9wgaBD.pdb has (at least) translational problems. Reordered lit - no good picture of real structure. 1wgc 2.2 dimer - 2 chains given; complex with N-Acetylneuraminyllactose; isolectin 1 2wgc 2.2 dimer - 2 chains given; complex with N-Acetylneuraminyllactose; isolectin 2 Xylose Isomerase (Arthrobacter strain B3728) 1xia 2.3 CA tetramer - 2 chains given; all residues UNK 4xia 2.3 tetramer - 2 chains given; complex with inhibitor sorbitol 5xia 2.5 tetramer - 2 chains given; complex with inhibitor xylitol Xylose Isomerase (Streptomyces rubiginosus) 2xia 3.5 CA tetramer - 2 chains given; all residues UNK Xylose Isomerase (Streptomyces olivochromogenes) 3xia 3.0 dimer or tetramer - 1 chain given 3xiaw made; looks like one Insight makes -- no tetrameric picture in lit; re-ordered literature Zinc Finger (Xenopus lavis) 1znf NMR monomer - 37 chains given; model 1 to be used for geometry