5DLC | pdb_00005dlc

X-ray Crystal Structure of a Pyridoxine 5-prime-phosphate synthase from Pseudomonas aeruginosa

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)
A	d5dlca_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d5dlcb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
C	d5dlcc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d5dlcd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Pyridoxine 5'-phosphate synthase	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pyridoxine 5'-phosphate synthase	8074919	4003313	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pyridoxine 5'-phosphate synthase	8074920	3000586	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8074920	3000586	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8074920	3000586	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pyridoxine 5'-phosphate synthase	8074920	3000586	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)
A	PdxJ	e5dlcA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
B	PdxJ	e5dlcB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
C	PdxJ	e5dlcC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)
D	PdxJ	e5dlcD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PdxJ	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Pyridoxine 5'-phosphate synthase	transferase activity, transferring nitrogenous groups pyridoxine 5'-phosphate synthase activity transferase activity catalytic activity	vitamin B6 biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process pyridine-containing compound biosynthetic process vitamin biosynthetic process pyridoxine biosynthetic process vitamin metabolic process pyridoxine metabolic process biosynthetic process pyridine-containing compound metabolic process vitamin B6 metabolic process metabolic process cellular process small molecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036130	Pyridoxine 5'-phosphate synthase	Homologous Superfamily
A, B, C, D	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D	IPR004569	Pyridoxal phosphate (active vitamin B6) biosynthesis PdxJ	Family

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.