4ECL | pdb_00004ecl

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
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)
D	SmpA_OmlA	e4eclD1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
C	SmpA_OmlA	e4eclC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
B	SmpA_OmlA	e4eclB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
A	APH	e4eclA1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: APH	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

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

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 (4.0.1)

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 (4.0.1)

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 anion binding heterocyclic compound binding small molecule binding acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity isomerase activity racemase and epimerase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity catalytic activity 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 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 response to stimulus response to chemical response to antibiotic 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 biosynthetic process D-amino acid biosynthetic process metabolic process cellular process D-alanine biosynthetic process alanine metabolic process alpha-amino acid biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.