6XBE | pdb_00006xbe

Structure of NDM-1 in complex with macrocycle inhibitor NDM1i-1F

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth D]	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8097724	3001057	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8097724	3001057	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8097724	3001057	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8097724	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)
G [auth D]	Lactamase_B	e6xbeD1	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)
E [auth C]	Lactamase_B	e6xbeC1	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)
C [auth B]	Lactamase_B	e6xbeB1	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)
A	Lactamase_B	e6xbeA1	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)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C], G [auth D]	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
B [auth F], D [auth G], F [auth H], H [auth I]	macrocycle inhibitor NDM1i-1F	-	-	-
A, C [auth B], E [auth C], G [auth D]	BlaNDM-4_1_JQ348841	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 ion binding binding metal ion binding small molecule binding	antibiotic metabolic process catabolic process metabolic process cellular process antibiotic catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B], E [auth C], G [auth D]	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, C [auth B], E [auth C], G [auth D]	IPR001279	Metallo-beta-lactamase	Domain
A, C [auth B], E [auth C], G [auth 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.