4RM5 | pdb_00004rm5

Structural and mechanistic insights into NDM-1 catalyzed hydrolysis of cephalosporins

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4rm5d_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
C	d4rm5c_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
B	d4rm5b_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
A	d4rm5a_	Alpha and beta proteins (a+b)	Metallo-hydrolase/oxidoreductase	Metallo-hydrolase/oxidoreductase	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	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	8061883	3001057	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061883	3001057	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061883	3001057	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metallo-hydrolase/oxidoreductase	8061883	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	Arf	e4rm5D1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: Arf	ECOD (develop294)
C	Arf	e4rm5C1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: Arf	ECOD (develop294)
B	Arf	e4rm5B1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: Arf	ECOD (develop294)
A	Arf	e4rm5A1	A: alpha bundles	X: thumb domain in bacteriophage RB69-like DNA polymerase I	H: thumb domain in bacteriophage RB69-like DNA polymerase I	T: thumb domain in bacteriophage RB69-like DNA polymerase I	F: Arf	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 (4.3.0)
C	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)
A	3.60.15.10	Alpha Beta	4-Layer Sandwich	Metallo-beta-lactamase	Chain A	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Beta-lactamase NDM-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, 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.