6LF4 | pdb_00006lf4

Crystal structure of VMB-1 bound to hydrolyzed meropenem

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6lf4d_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Vibrio alginolyticus ) [TaxId: 663 ],	SCOPe (2.08)
C	d6lf4c_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Vibrio alginolyticus ) [TaxId: 663 ],	SCOPe (2.08)
B	d6lf4b_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Vibrio alginolyticus ) [TaxId: 663 ],	SCOPe (2.08)
A	d6lf4a_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Vibrio alginolyticus ) [TaxId: 663 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8095421	3001057	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8095421	3001057	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8095421	3001057	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8095421	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)
D	Lactamase_B	e6lf4D1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)
C	Lactamase_B	e6lf4C1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)
B	Lactamase_B	e6lf4B1	A: alpha bundles	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Lactamase_B	ECOD (develop294)
A	IF-2	e6lf4A1	A: alpha bundles	X: Rubredoxin-like	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: IF-2	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (utative)
C	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (utative)
B	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (utative)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (utative)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B, C, D	ARO:3005015	VMB-1	Vibrio metallo-B-lactamase 1, also known as VMB-1, is carbapenemase beta-lactamase that is found in plasmid pVB1796 from Vibrio alginolyticus.	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:3005014	VMB beta-lactamase	carbapenem, cephalosporin, penicillin beta-lactam	antibiotic inactivation	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	VMB-1 metallo-beta-lactamase	beta-lactamase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds cation binding transition metal ion binding zinc ion 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, B, C, D	IPR001018	Beta-lactamase, class-B, conserved site	Conserved Site
A, B, C, D	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, B, C, D	IPR058199	Metallo-beta-lactamase type 2/VIM/IMP-1	Family
A, B, C, D	IPR001279	Metallo-beta-lactamase	Domain
A, B, C, D	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.