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(-) Description

Title :  YEAST GLUTATHIONE SYNTHASE BOUND TO GAMMA-GLUTAMYL-CYSTEINE, AMP-PNP AND 2 MAGNESIUM IONS
 
Authors :  A. Gogos, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  14 Jun 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Amine/Carboxylate Ligase, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Gogos, L. Shapiro
Large Conformational Changes In The Catalytic Cycle Of Glutathione Synthase
Structure V. 10 1669 2002
PubMed-ID: 12467574  |  Reference-DOI: 10.1016/S0969-2126(02)00906-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTATHIONE SYNTHETASE
    ChainsA, B
    EC Number6.3.2.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28TEV
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneGSH2
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymGLUTATHIONE SYNTHASE, GSH SYNTHETASE, GSH-S

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric/Biological Unit (4, 15)
No.NameCountTypeFull Name
13GC2Ligand/IonGAMMA-GLUTAMYLCYSTEINE
2ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3MG4Ligand/IonMAGNESIUM ION
4SO47Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:146 , ANP A:504 , HOH A:2517 , HOH A:2585 , HOH A:2603BINDING SITE FOR RESIDUE MG A 502
02AC2SOFTWAREGLU B:1146 , ANP B:1504 , HOH B:2559 , HOH B:2673 , HOH B:2674BINDING SITE FOR RESIDUE MG B 1502
03AC3SOFTWAREGLU A:146 , GLU A:386 , ANP A:504 , HOH A:2001BINDING SITE FOR RESIDUE MG A 503
04AC4SOFTWAREGLU B:1146 , GLU B:1386 , ANP B:1504 , HOH B:2732BINDING SITE FOR RESIDUE MG B 1503
05AC5SOFTWARELYS A:136 , LYS A:137 , ARG A:273 , HOH A:2705 , HOH A:2707BINDING SITE FOR RESIDUE SO4 A 506
06AC6SOFTWAREARG A:163 , HOH A:2388 , HOH A:2747BINDING SITE FOR RESIDUE SO4 A 507
07AC7SOFTWARELYS A:113 , SER A:114 , ARG B:1366 , ARG B:1370 , HOH B:2579BINDING SITE FOR RESIDUE SO4 B 508
08AC8SOFTWARELYS B:1136 , LYS B:1137 , ARG B:1273 , HOH B:2699BINDING SITE FOR RESIDUE SO4 B 509
09AC9SOFTWAREARG B:1163 , HOH B:2478 , HOH B:2528BINDING SITE FOR RESIDUE SO4 B 510
10BC1SOFTWAREGLY A:389 , ASN A:391 , TYR A:393 , ANP A:504 , HOH A:2581BINDING SITE FOR RESIDUE SO4 A 511
11BC2SOFTWAREGLY B:1389 , ASN B:1390 , ASN B:1391 , TYR B:1393 , ANP B:1504 , HOH B:2374BINDING SITE FOR RESIDUE SO4 B 512
12BC3SOFTWAREVAL A:145 , GLU A:146 , LYS A:324 , LYS A:382 , GLU A:386 , GLY A:387 , ASN A:391 , TYR A:393 , MET A:415 , GLU A:416 , LEU A:417 , ILE A:418 , GLU A:442 , LYS A:469 , 3GC A:501 , MG A:502 , MG A:503 , SO4 A:511 , HOH A:2013 , HOH A:2107 , HOH A:2233 , HOH A:2353 , HOH A:2517 , HOH A:2585 , HOH A:2603 , HOH A:2724BINDING SITE FOR RESIDUE ANP A 504
13BC4SOFTWARESO4 B:512 , VAL B:1145 , GLU B:1146 , LYS B:1324 , VAL B:1380 , LYS B:1382 , GLU B:1386 , ASN B:1391 , TYR B:1393 , MET B:1415 , GLU B:1416 , LEU B:1417 , ILE B:1418 , GLU B:1442 , LYS B:1469 , 3GC B:1501 , MG B:1502 , MG B:1503 , HOH B:2189 , HOH B:2372 , HOH B:2376 , HOH B:2554 , HOH B:2559 , HOH B:2673 , HOH B:2674BINDING SITE FOR RESIDUE ANP B 1504
14BC5SOFTWAREARG A:128 , ASN A:148 , VAL A:150 , SER A:151 , VAL A:152 , SER A:153 , GLU A:228 , ASN A:230 , GLN A:234 , ARG A:285 , TYR A:288 , ARG A:467 , ANP A:504 , HOH A:2298 , HOH A:2517 , HOH A:2724BINDING SITE FOR RESIDUE 3GC A 501
15BC6SOFTWAREARG B:1128 , VAL B:1150 , SER B:1151 , VAL B:1152 , SER B:1153 , GLU B:1228 , ASN B:1230 , GLN B:1234 , ARG B:1285 , TYR B:1288 , ARG B:1467 , ANP B:1504 , HOH B:2286 , HOH B:2674BINDING SITE FOR RESIDUE 3GC B 1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M0W)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:313 -Pro A:314
2Ala B:1313 -Pro B:1314

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M0W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1M0W)

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YOL049W1YOL049W.1XV:238618-2400931476GSHB_YEAST1-4914912A:6-491 (gaps)
B:1005-1491 (gaps)
486
487

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:481
 aligned with GSHB_YEAST | Q08220 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:486
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      
          GSHB_YEAST      6 PSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQREGGGNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY  491
               SCOP domains d1m0wa2 A:6-210,A:324-491 Eukaryotic glutathione synthetase ATP-binding domain                                                                                                                               -----d1m0wa1 A:216-323 Eukaryotic glutathione synthetase, substrate-binding domain                               d1m0wa2 A:6-210,A:324-491 Eukaryotic glutathione synthetase ATP-binding domain                                                                                           SCOP domains
               CATH domains -1m0wA01 A:7-51,A:160-188,A:427-437           1m0wA02     1m0wA03 A:64-115,A:323-355                          --1m0wA02 A:52-63,A:118-159,A:438-491       1m0wA01                      1m0wA04 A:189-322  [co     de=3.40.50.1760, no name defined]                                                                          1m0wA03 A:64-115,A:323-355       1m0wA05 A:356-417  [code=3.30.1490.50, no name defined]       ---------1m0wA01    1m0wA02 A:52-63,A:118-159,A:438-491                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.ee...hhhhh..eeee..ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhh..........eeeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhh..........hhhhh...hhhhhhhhhhhhhhhhhhhh.-----...eeeeee.....hhhhhhhhhhhhhhh....eeeehhhhhhhheee......eee.....eeeeeeee...hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhh....eee...hhhhhhhhhhhhhh...eeeee........ee..hhhhhhhhhhhhhhh.eeeee...........eee..eee....eeeeeeeeeeee....eeeeeeeeeeeeee..eee..eeee..eee..eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:6-491 (gaps) UniProt: 1-491 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                              Transcript 1
                1m0w A    6 PSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQ-----SDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQREGGGNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY  491
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205    |    -|      225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485      
                                                                                                                                                                                                                                      210   216                                                                                                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:479
 aligned with GSHB_YEAST | Q08220 from UniProtKB/Swiss-Prot  Length:491

    Alignment length:487
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       
          GSHB_YEAST      5 PPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQSSSTTSDPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQREGGGNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY  491
               SCOP domains d1m0wb2 B:1005-1210,B:1324-1491 Eukaryotic glutathione synthetase ATP-binding domain                                                                                                                                d1m0wb1 B:1217-1323 Eukaryotic glutathione synthetase, substrate-binding domain                            d1m0wb2 B:1005-1210,B:1324-1491 Eukaryotic glutathione syntheta  se ATP-binding domain                                                                                   SCOP domains
               CATH domains --1m0wB01 B:1007-1051,B:1160-1188,B:1427-1437  1m0wB02     1m0wB03 B:1064-1115,B:1323-1355                     --1m0wB02 ATP-grasp fold, B domain          1m0wB01                      1m0wB04 B:1189-1322  [      code=3.40.50.1760, no name defined]                                                                       1m0wB03 B:1064-1115,B:1323-1355  1m0wB05 B:1356-1417  [code=3.30  .1490.50, no name defined]   ---------1m0wB01    1m0wB02 B:1052-1063,B:1118-1159,B:1438-1491            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.ee...hhhhh..eeee..ee...eeeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhh..........eeeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhhhh..........hhhhh...hhhhhhhhhhhhhhhhhhhh.------..eeeeee.....hhhhhhhhhhhhhhhhh..eeeehhhhhhhheee......eee.....eeeeeeee...hhhhh.hhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhh...ee....hhhhhhhhhhhhhh...eeeee...--...ee..hhhhhhhhhhhhhhh.eeeee...........eee..eee....eeeeeeeeeeee....eeeeeeeeeeeeee..eee..eeee..eee..eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1005-1491 (gaps) UniProt: 1-491 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                                           Transcript 1
                1m0w B 1005 PPSKDQLNELIQEVNQWAITNGLSMYPPKFEENPSNASVSPVTIYPTPIPRKCFDEAVQIQPVFNELYARITQDMAQPDSYLHKTTEALALSDSEFTGKLWSLYLATLKSAQYKKQNFRLGIFRSDYLIDKKKGTEQIKQVEFNTVSVSFAGLSEKVDRLHSYLNRANKYDPKGPIYNDQNMVISDSGYLLSKALAKAVESYKSQQ------DPIVAFIVQRNERNVFDQKVLELNLLEKFGTKSVRLTFDDVNDKLFIDDKTGKLFIRDTEQEIAVVYYRTGYTTTDYTSEKDWEARLFLEKSFAIKAPDLLTQLSGSKKIQQLLTDEGVLGKYISDAEKKSSLLKTFVKIYPLDDTKLGREGKRLALSEPSKYVLKPQRE--GNNVYKENIPNFLKGIEERHWDAYILMELIEPELNENNIILRDNKSYNEPIISELGIYGCVLFNDEQVLSNEFSGSLLRSKFNTSNEGGVAAGFGCLDSIILY 1491
                                  1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204     |   -  |   1224      1234      1244      1254      1264      1274      1284      1294      1304      1314      1324      1334      1344      1354      1364      1374      1384 |  | 1394      1404      1414      1424      1434      1444      1454      1464      1474      1484       
                                                                                                                                                                                                                                      1210   1217                                                                                                                                                                     1386  |                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                         1389                                                                                                      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (5, 10)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1M0W)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GSHB_YEAST | Q08220)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043295    glutathione binding    Interacting selectively and non-covalently with glutathione; a tripeptide composed of the three amino acids cysteine, glutamic acid and glycine.
    GO:0004363    glutathione synthase activity    Catalysis of the reaction: L-gamma-glutamyl-L-cysteine + ATP + glycine = ADP + glutathione + 2 H(+) + phosphate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GSHB_YEAST | Q082201m0t

(-) Related Entries Specified in the PDB File

1m0t 1M0T IS YEAST GLUTATHIONE SYNTHASE. RELATED ID: NYSGXRC-P102 RELATED DB: TARGETDB
2hgs 2HGS IS HUMAN GLUTATHIONE SYNTHETASE.