5NDE | pdb_00005nde

Crystal structure of metallo-beta-lactamase SPM-1 in space group P4222

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)
B	d5ndeb_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
A	d5ndea_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	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)
B	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8086659	3001057	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8086659	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)
B	7tm_1	e5ndeB1	A: a/b three-layered sandwiches	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase/SAICAR synthase/ATP-grasp	T: Protein kinase	F: 7tm_1	ECOD (v294.1)
A	UQ_con	e5ndeA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A, B	ARO:3003793	SPM-1	Plasmid-mediated SPM metallo-beta-lactamase conferring resistance to carbapenem. Originally isolated from Pseudomonas aeruginosa. Responsible for carbapenem-resistant Pseudomonas aeruginosa (CRPA) outbreaks in Brazil.	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:3000580	SPM beta-lactamase	carbapenem	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	Beta-lactamase IMP-1	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	IPR001018	Beta-lactamase, class-B, conserved site	Conserved Site
A, B	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, B	IPR058199	Metallo-beta-lactamase type 2/VIM/IMP-1	Family
A, B	IPR001279	Metallo-beta-lactamase	Domain
A, B	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.