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3QXJ

Crystal structure of dethiobiotin synthetase (BioD) from Helicobacter pylori complexed with GTP

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0000287molecular_functionmagnesium ion binding
A0004141molecular_functiondethiobiotin synthase activity
A0005524molecular_functionATP binding
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0009102biological_processbiotin biosynthetic process
A0016874molecular_functionligase activity
A0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues20
DetailsBINDING SITE FOR RESIDUE GTP A 221
ChainResidue
ATHR9
AGLU116
AGLN167
AMG224
AEDO232
AHOH279
AHOH283
AHOH284
AHOH374
AHOH468
AHOH492
AASN10
AHOH520
AALA11
AGLY12
ALYS13
ATHR14
ATHR15
ALYS35
AASP50

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 222
ChainResidue
AASN42
AASP43
AARG74
AHIS76
AHOH364
AHOH451

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 223
ChainResidue
AASN130
AASP133
AHIS166
AHOH523

site_idAC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MG A 224
ChainResidue
ATHR14
AASP50
AGLU116
AGTP221
AHOH374

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 225
ChainResidue
AASN25
AGLY28
ALYS30
ALEU61
AHOH310

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 226
ChainResidue
AHIS0
AMET1
ALYS139
ALYS141
ASER220

site_idAC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 227
ChainResidue
ALYS171
ATHR181
ASER185
AVAL211
AHOH369
AHOH413
AHOH512

site_idAC8
Number of Residues10
DetailsBINDING SITE FOR RESIDUE NO3 A 228
ChainResidue
ASER5
AALA6
ALYS13
AGLY117
AALA118
AGLY119
AGLY120
ALEU121
AMET131
AHOH391

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 229
ChainResidue
ALEU168
AASP169
ATYR170
AASN200
AHOH493

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 230
ChainResidue
AGLU87
AGLU88
ALEU217
AHOH448
AHOH481
AHOH484

site_idBC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 231
ChainResidue
AASN8
AASN149

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 232
ChainResidue
ALYS35
AGLU38
ATHR39
AALA118
AGTP221
AHOH492
AHOH520

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues6
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI7
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QY0","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI8
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI9
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00336","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3MLE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXH","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI10
Number of Residues1
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"22284390","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3QXC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3QXS","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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