6YRP | pdb_00006yrp

Crystal Structure of the VIM-2 Acquired Metallo-beta-Lactamase in Complex with JMV-4690 (Cpd 31)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
Protein Family Annotation
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	d6yrpa_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	Zn metallo-beta-lactamase	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	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061867	3001057	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	Lactamase_B	e6yrpA1	A: a+b four layers	X: Metallo-hydrolase/oxidoreductase (From Topology)	H: Metallo-hydrolase/oxidoreductase (From Topology)	T: Metallo-hydrolase/oxidoreductase	F: Lactamase_B	ECOD (1.6)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A	ARO:3002287	VIM-17	VIM-17 is a beta-lactamase found in Pseudomonas aeruginosa.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A	ARO:3000021	VIM beta-lactamase	carbapenem, cephalosporin, penicillin beta-lactam	antibiotic inactivation	CARD (4.0.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00753	Metallo-beta-lactamase superfamily (Lactamase_B)	Metallo-beta-lactamase superfamily		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Metallo-beta-lactamase VIM-2-like protein	hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	antibiotic metabolic process catabolic process metabolic process cellular process antibiotic catabolic process response to stimulus response to chemical response to antibiotic	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A	IPR049721	Metallo-beta-lactamase VIM-1/2, metallo-hydrolase domain	Domain
A	IPR001279	Metallo-beta-lactamase	Domain
A	IPR050855	Metallo-beta-lactamase type 2-like	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.