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3GDL

Crystal structure of the orotidine 5'-monophosphate decarboxylase from Saccharomyces cerevisiae complexed with 6-azauridine 5'-monophosphate

Functional Information from GO Data
ChainGOidnamespacecontents
A0004590molecular_functionorotidine-5'-phosphate decarboxylase activity
A0005829cellular_componentcytosol
A0006207biological_process'de novo' pyrimidine nucleobase biosynthetic process
A0006221biological_processpyrimidine nucleotide biosynthetic process
A0006222biological_processUMP biosynthetic process
A0016829molecular_functionlyase activity
A0016831molecular_functioncarboxy-lyase activity
A0044205biological_process'de novo' UMP biosynthetic process
B0004590molecular_functionorotidine-5'-phosphate decarboxylase activity
B0005829cellular_componentcytosol
B0006207biological_process'de novo' pyrimidine nucleobase biosynthetic process
B0006221biological_processpyrimidine nucleotide biosynthetic process
B0006222biological_processUMP biosynthetic process
B0016829molecular_functionlyase activity
B0016831molecular_functioncarboxy-lyase activity
B0044205biological_process'de novo' UMP biosynthetic process
Functional Information from PDB Data
site_idAC1
Number of Residues21
DetailsBINDING SITE FOR RESIDUE UP6 A 301
ChainResidue
ASER35
AGLN215
ATYR217
AGLY234
AARG235
AHOH274
AHOH278
AHOH283
AHOH306
AHOH358
BASP96
AASP37
BILE97
BTHR100
ALYS59
AHIS61
AASP91
ALYS93
ALEU153
ASER154
APRO202

site_idAC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE UP6 B 301
ChainResidue
AASP96
AILE97
ATHR100
BSER35
BASP37
BLYS59
BHIS61
BASP91
BLYS93
BLEU153
BSER154
BPRO202
BGLN215
BTYR217
BGLY234
BARG235
BHOH282
BHOH287
BHOH294
BHOH314
BHOH387

Functional Information from PROSITE/UniProt
site_idPS00156
Number of Residues14
DetailsOMPDECASE Orotidine 5'-phosphate decarboxylase active site. LFeDrKfaDIGnTV
ChainResidueDetails
ALEU88-VAL101

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsACT_SITE: Proton donor
ChainResidueDetails
ALYS93
BLYS93

site_idSWS_FT_FI2
Number of Residues10
DetailsBINDING:
ChainResidueDetails
AASP37
BARG235
ALYS59
AASP91
ATYR217
AARG235
BASP37
BLYS59
BASP91
BTYR217

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: N-acetylserine => ECO:0007744|PubMed:22814378
ChainResidueDetails
ASER2
BSER2

site_idSWS_FT_FI4
Number of Residues8
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:12872131
ChainResidueDetails
ALYS93
ALYS209
ALYS253
BLYS93
BLYS209
BLYS253

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1dbt
ChainResidueDetails
AASP91
ALYS93

site_idCSA2
Number of Residues2
DetailsAnnotated By Reference To The Literature 1dbt
ChainResidueDetails
BASP91
BLYS93

site_idCSA3
Number of Residues4
DetailsAnnotated By Reference To The Literature 1dbt
ChainResidueDetails
ALYS59
AASP96
AASP91
ALYS93

site_idCSA4
Number of Residues4
DetailsAnnotated By Reference To The Literature 1dbt
ChainResidueDetails
BLYS59
BASP96
BASP91
BLYS93

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PDB entries from 2025-07-02

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