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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

4H3D

1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.

Functional Information from GO Data
ChainGOidnamespacecontents
A0003855molecular_function3-dehydroquinate dehydratase activity
A0008652biological_processamino acid biosynthetic process
A0009073biological_processaromatic amino acid family biosynthetic process
A0009423biological_processchorismate biosynthetic process
A0016829molecular_functionlyase activity
A0046279biological_process3,4-dihydroxybenzoate biosynthetic process
B0003855molecular_function3-dehydroquinate dehydratase activity
B0008652biological_processamino acid biosynthetic process
B0009073biological_processaromatic amino acid family biosynthetic process
B0009423biological_processchorismate biosynthetic process
B0016829molecular_functionlyase activity
B0046279biological_process3,4-dihydroxybenzoate biosynthetic process
C0003855molecular_function3-dehydroquinate dehydratase activity
C0008652biological_processamino acid biosynthetic process
C0009073biological_processaromatic amino acid family biosynthetic process
C0009423biological_processchorismate biosynthetic process
C0016829molecular_functionlyase activity
C0046279biological_process3,4-dihydroxybenzoate biosynthetic process
D0003855molecular_function3-dehydroquinate dehydratase activity
D0008652biological_processamino acid biosynthetic process
D0009073biological_processaromatic amino acid family biosynthetic process
D0009423biological_processchorismate biosynthetic process
D0016829molecular_functionlyase activity
D0046279biological_process3,4-dihydroxybenzoate biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PGE A 301
ChainResidue
AGLY88
APHE146
AHOH606
site_idAC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEG A 302
ChainResidue
AILE24
AARG49
AGLN237
AHOH602
AHOH623
site_idAC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SHL A 303
ChainResidue
AHIS144
ALYS171
AMET204
AARG214
APHE226
AGLN237
AHOH592
AHOH594
AHOH595
AHOH602
AARG83
site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PEG B 301
ChainResidue
BVAL86
BGLY88
BHOH521
site_idAC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SHL B 302
ChainResidue
BARG83
BHIS144
BLYS171
BMET204
BARG214
BPHE226
BGLN237
BHOH450
BHOH574
site_idAC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT B 303
ChainResidue
BASP145
BPHE146
BASN147
site_idAC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PGE C 301
ChainResidue
CPHE146
CHOH538
CHOH611
site_idAC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SHL C 302
ChainResidue
CARG83
CHIS144
CLYS171
CMET204
CARG214
CPHE226
CGLN237
CHOH515
CHOH516
site_idAC9
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SHL D 301
ChainResidue
DARG83
DHIS144
DLYS171
DMET204
DARG214
DPHE226
DGLN237
DHOH437
DHOH486
DHOH525
DHOH537
site_idBC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE ACT D 302
ChainResidue
DGLU87
DPHE119
DASN143
site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ACT D 303
ChainResidue
DPHE146
DASN147
DHOH461
DHOH551
Functional Information from PROSITE/UniProt
site_idPS01028
Number of Residues31
DetailsDEHYDROQUINASE_I Dehydroquinase class I active site. DVELfmgdevidevvnfahkkevkVIiSNHD
ChainResidueDetails
AASP115-ASP145
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsActive site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2012","submissionDatabase":"PDB data bank","title":"1.95 Angstrom crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent modified comenic acid.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"],"authors":["Minasov G.","Light S.H.","Shuvalova L.","Duban M.E.","Dubrovska I.","Winsor J.","Papazisi L.","Anderson W.F."]}}]}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues4
DetailsActive site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2012","submissionDatabase":"PDB data bank","title":"1.95 Angstrom crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent modified comenic acid.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"],"authors":["Minasov G.","Light S.H.","Shuvalova L.","Duban M.E.","Dubrovska I.","Winsor J.","Papazisi L.","Anderson W.F."]}}]}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues9
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00214","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21087925","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2012","submissionDatabase":"PDB data bank","title":"1.95 Angstrom crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent modified comenic acid.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"],"authors":["Minasov G.","Light S.H.","Shuvalova L.","Duban M.E.","Dubrovska I.","Winsor J.","Papazisi L.","Anderson W.F."]}}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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