5YPI | pdb_00005ypi

Crystal structure of NDM-1 bound to hydrolyzed imipenem representing an EI1 complex

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5ypia_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d5ypib_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d5ypic_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d5ypid_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d5ypie_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d5ypif_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d5ypig_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d5ypih_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	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	8061885	3001057	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	3001057	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	3001057	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	3001057	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	3001057	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	3001057	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	3001057	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061885	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	e5ypiA1	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)
B	Lactamase_B	e5ypiB1	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	Lactamase_B	e5ypiC1	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)
D	Lactamase_B	e5ypiD1	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	Lactamase_B	e5ypiE1	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)
F	Lactamase_B	e5ypiF1	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)
G	Lactamase_B	e5ypiG1	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)
H	Lactamase_B	e5ypiH1	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)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
B	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
C	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
D	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
E	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
F	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
G	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)
H	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, B, C, D, E A, B, C, D, E, F, G, H	Metallo-beta-lactamase NDM-1	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, B, C, D, E A, B, C, D, E, F, G, H	IPR036866	Ribonuclease Z/Hydroxyacylglutathione hydrolase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001279	Metallo-beta-lactamase	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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.