7NRJ

Crystal Structure of a Class D carbapenemase complexed with iodide

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
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)
A [auth AAA]	SCOP2 Family	beta-Lactamase/D-ala carboxypeptidase	8106815	4002685	SCOP2 (2022-06-29)
A [auth AAA]	SCOP2 Superfamily	beta-lactamase/transpeptidase-like	8106816	3001604	SCOP2 (2022-06-29)
C [auth CCC]	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8106816	3001604	SCOP2B (2022-06-29)
D [auth DDD]	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8106816	3001604	SCOP2B (2022-06-29)
B [auth BBB]	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8106816	3001604	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 [auth AAA]	Transpeptidase_1st	e7nrjAAA2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st	ECOD (1.6)
A [auth AAA]	Transpeptidase_2nd_1	e7nrjAAA1	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd_1	ECOD (1.6)
C [auth CCC]	Transpeptidase_1st	e7nrjCCC2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st	ECOD (1.6)
C [auth CCC]	Transpeptidase_2nd_1	e7nrjCCC1	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd_1	ECOD (1.6)
D [auth DDD]	Transpeptidase_1st	e7nrjDDD1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st	ECOD (1.6)
D [auth DDD]	Transpeptidase_2nd_1	e7nrjDDD2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd_1	ECOD (1.6)
B [auth BBB]	Transpeptidase_1st	e7nrjBBB2	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st	ECOD (1.6)
B [auth BBB]	Transpeptidase_2nd_1	e7nrjBBB1	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd_1	ECOD (1.6)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	ARO:3001782	OXA-48	OXA-48 is a beta-lactamase found in Klebsiella pneumoniae.	CARD (3.3.0)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	ARO:3007721	OXA-48-like beta-lactamase	carbapenem, penam	antibiotic inactivation	CARD (3.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	PF00905	Penicillin binding protein transpeptidase domain (Transpeptidase)	Penicillin binding protein transpeptidase domain	The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	Beta-lactamase	amide binding organic acid binding binding ion binding organic cyclic compound binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding beta-lactamase activity hydrolase activity amide binding organic acid binding binding ion binding organic cyclic compound binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding 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	antibiotic metabolic process catabolic process metabolic process cellular process antibiotic catabolic process cellular component organization cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization response to stimulus response to chemical response to antibiotic	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR050515	Bacterial Transpeptidases and Beta-Lactamases	Family
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR002137	Beta-lactamase, class-D active site	Active Site

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.