4OAK | pdb_00004oak

Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II)

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)
B		e4oakB1	A: MHC antigen-recognition domain	X: MHC antigen-recognition domain	H: MHC antigen-recognition domain	T: PolyA_pol	F:	ECOD (20:10:01)
A		e4oakA1	A: MHC antigen-recognition domain	X: MHC antigen-recognition domain	H: MHC antigen-recognition domain	T: PolyA_pol	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
A	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B	ARO:3002966	vanXY gene in vanC cluster	Also known as vanXYC, is a vanXY variant found in the vanC 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	ARO:3000496	vanXY	glycopeptide antibiotic	antibiotic target alteration	CARD (4.0.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02557	D-alanyl-D-alanine carboxypeptidase (VanY)	D-alanyl-D-alanine carboxypeptidase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	D,D-dipeptidase/D,D-carboxypeptidase	peptidase activity catalytic activity, acting on a protein hydrolase activity exopeptidase activity catalytic activity carboxypeptidase activity D-Ala-D-Ala dipeptidase activity dipeptidase activity cation binding ion binding binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process response to stimulus response to chemical response to antibiotic	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR058233	D,D-carboxypeptidase/D,D-dipeptidase VanXY	Family
A, B	IPR052179	D-alanyl-D-alanine carboxypeptidase-like	Family
A, B	IPR009045	Peptidase M74/Hedgehog-like, zinc-binding domain superfamily	Homologous Superfamily
A, B	IPR003709	D-alanyl-D-alanine carboxypeptidase-like, core 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.