Annotations: 3IEB

Crystal structure of 3-keto-L-gulonate-6-phosphate decarboxylase from Vibrio cholerae O1 biovar El Tor str. N16961

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d3iebe_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
D	d3iebd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
C	d3iebc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
B	d3iebb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)
A	d3ieba_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Vibrio cholerae ) [TaxId: 666 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8080786	3000216	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8080786	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8080786	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8080786	3000216	SCOP2B (2022-06-29)
A	SCOP2 Family	Decarboxylase	8080785	4003062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribulose-phoshate binding barrel	8080786	3000216	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	YgbB	e3iebE1	A: beta barrels	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.2)
D	YgbB	e3iebD1	A: beta barrels	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.2)
C	YgbB	e3iebC1	A: beta barrels	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.2)
B	YgbB	e3iebB1	A: beta barrels	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: YgbB	ECOD (v294.2)
A	Esterase	e3iebA1	A: beta barrels	X: Spectrin repeat-like	H: SH3	T: SH3	F: Esterase	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF00215	Orotidine 5'-phosphate decarboxylase / HUMPS family (OMPdecase)	Orotidine 5'-phosphate decarboxylase / HUMPS family	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly ...	This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to Pfam:PF00834.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Hexulose-6-phosphate synthase SgbH	3-dehydro-L-gulonate-6-phosphate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity cation binding ion binding binding metal ion binding small molecule binding orotidine-5'-phosphate decarboxylase activity	pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process cellular process pyrimidine-containing compound biosynthetic process pyrimidine-containing compound metabolic process nucleobase biosynthetic process pyrimidine nucleobase biosynthetic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process biosynthetic process nucleobase-containing small molecule metabolic process nucleobase metabolic process 'de novo' pyrimidine nucleobase biosynthetic process small molecule metabolic process metabolic process cellular process pyrimidine-containing compound biosynthetic process monosaccharide metabolic process carbohydrate metabolic process catabolic process oxoacid metabolic process carbohydrate catabolic process carboxylic acid metabolic process organic acid catabolic process organic acid metabolic process L-ascorbic acid catabolic process L-ascorbic acid metabolic process vitamin catabolic process vitamin metabolic process water-soluble vitamin catabolic process carboxylic acid catabolic process lactone metabolic process lactone catabolic process small molecule catabolic process monosaccharide catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR041710	HPS/KGPDC domain	Domain
A, B, C, D, E	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B, C, D, E	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E	IPR001754	Orotidine 5'-phosphate decarboxylase domain	Domain

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.