3EXS | pdb_00003exs

Crystal structure of KGPDC from Streptococcus mutans in complex with D-R5P

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d3exsd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	3-keto-L-gulonate 6-phosphate decarboxylase	(Streptococcus mutans ) [TaxId: 1309 ],	SCOPe (2.08)
C	d3exsc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	3-keto-L-gulonate 6-phosphate decarboxylase	(Streptococcus mutans ) [TaxId: 1309 ],	SCOPe (2.08)
B	d3exsb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	3-keto-L-gulonate 6-phosphate decarboxylase	(Streptococcus mutans ) [TaxId: 1309 ],	SCOPe (2.08)
A	d3exsa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Decarboxylase	3-keto-L-gulonate 6-phosphate decarboxylase	(Streptococcus mutans ) [TaxId: 1309 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8063390	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8063390	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8063390	3000216	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8063390	3000216	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	MTHFR	e3exsD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
C	MTHFR	e3exsC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
B	MTHFR	e3exsB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)
A	MTHFR	e3exsA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: MTHFR	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RmpD (Hexulose-6-phosphate synthase)	3-dehydro-L-gulonate-6-phosphate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity hexulose-6-phosphate synthase activity aldehyde-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 one-carbon metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

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

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.