4ECL

Crystal structure of the cytoplasmic domain of vancomycin resistance serine racemase VanTg

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ala_racemase_C	e4eclA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ala_racemase_C	ECOD (1.6)
A	Ala_racemase_N	e4eclA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ala_racemase_N	ECOD (1.6)
B	Ala_racemase_C	e4eclB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ala_racemase_C	ECOD (1.6)
B	Ala_racemase_N	e4eclB2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ala_racemase_N	ECOD (1.6)
C	Ala_racemase_C	e4eclC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ala_racemase_C	ECOD (1.6)
C	Ala_racemase_N	e4eclC2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ala_racemase_N	ECOD (1.6)
D	Ala_racemase_C	e4eclD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ala_racemase_C	ECOD (1.6)
D	Ala_racemase_N	e4eclD2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ala_racemase_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
A	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
B	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
B	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
C	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
C	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)
D	2.40.37.10	Mainly Beta	Beta Barrel	Lyase, Ornithine Decarboxylase	Chain A, domain 1	CATH (4.3.0)
D	3.20.20.10	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Alanine racemase	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B, C, D	ARO:3002972	vanT gene in vanG cluster	Also known as vanTG, is a vanT variant found in the vanG gene cluster.	CARD (3.2.9)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A, B, C, D	ARO:3000372	vanT	glycopeptide antibiotic	antibiotic target alteration	CARD (3.2.9)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00842	Alanine racemase, C-terminal domain (Ala_racemase_C)	Alanine racemase, C-terminal domain	-	Domain
A, B, C, D	PF01168	Alanine racemase, N-terminal domain (Ala_racemase_N)	Alanine racemase, N-terminal domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Serine racemase	vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity racemase activity, acting on amino acids and derivatives vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity racemase activity, acting on amino acids and derivatives isomerase activity racemase and epimerase activity alanine racemase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity	response to stimulus response to chemical response to antibiotic cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis peptidoglycan metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis response to stimulus response to chemical response to antibiotic cellular biosynthetic process cell wall organization or biogenesis glycosaminoglycan metabolic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process cellular component biogenesis peptidoglycan metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis organonitrogen compound metabolic process cellular metabolic process macromolecule biosynthetic process peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process macromolecule metabolic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process D-alanine metabolic process carboxylic acid biosynthetic process non-proteinogenic amino acid metabolic process D-amino acid metabolic process small molecule metabolic process alanine biosynthetic process non-proteinogenic amino acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process amino acid biosynthetic process D-amino acid biosynthetic process D-alanine biosynthetic process alanine metabolic process alpha-amino acid biosynthetic process	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029066	PLP-binding barrel	Homologous Superfamily
A, B, C, D	IPR020622	Alanine racemase, pyridoxal-phosphate attachment site	Binding Site
A, B, C, D	IPR011079	Alanine racemase, C-terminal	Domain
A, B, C, D	IPR011248	Serine/alanine racemase	Family
A, B, C, D	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal	Homologous Superfamily
A, B, C, D	IPR001608	Alanine racemase, N-terminal	Domain
A, B, C, D	IPR000821	Alanine racemase	Family
A, B, C, D	IPR002656	Acyltransferase 3 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 R01GM133198.