6ZRJ | pdb_00006zrj

Crystal structure of class D Beta-lactamase OXA-48 in complex with ertapenem

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
AMR Gene: CARD Annotation
AMR Gene Family: CARD 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)
B	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	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)
B	Glyco_transf_41	e6zrjB1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
H	Glyco_transf_41	e6zrjH1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
G	Glyco_transf_41	e6zrjG1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
F	Glyco_transf_41	e6zrjF1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
E	Glyco_transf_41	e6zrjE1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
D	Glyco_transf_41	e6zrjD1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
C	Glyco_transf_41	e6zrjC1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)
A	Glyco_transf_41	e6zrjA1	A: alpha bundles	X: RNase A-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Glyco_transf_41	ECOD (develop294)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
B	ARO:3001782	OXA-48	OXA-48 is a beta-lactamase found in Klebsiella pneumoniae.	CARD (4.0.1)
B	ARO:3001782	OXA-48	OXA-48 is a beta-lactamase found in Klebsiella pneumoniae.	CARD (4.0.1)
A, C, D, E, F A, C, D, E, F, G, H	ARO:3001782	OXA-48	OXA-48 is a beta-lactamase found in Klebsiella pneumoniae.	CARD (4.0.1)
A, C, D, E, F A, C, D, E, F, G, H	ARO:3001782	OXA-48	OXA-48 is a beta-lactamase found in Klebsiella pneumoniae.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
B	ARO:3007721	OXA-48-like beta-lactamase	carbapenem, penicillin beta-lactam	antibiotic inactivation	CARD (4.0.1)
B	ARO:3007721	OXA-48-like beta-lactamase	carbapenem, penicillin beta-lactam	antibiotic inactivation	CARD (4.0.1)
A, C, D, E, F A, C, D, E, F, G, H	ARO:3007721	OXA-48-like beta-lactamase	carbapenem, penicillin beta-lactam	antibiotic inactivation	CARD (4.0.1)
A, C, D, E, F A, C, D, E, F, G, H	ARO:3007721	OXA-48-like beta-lactamase	carbapenem, penicillin beta-lactam	antibiotic inactivation	CARD (4.0.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Beta-lactamase	organic acid binding binding ion 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 organic acid binding binding ion 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	cell periphery cellular anatomical structure plasma membrane membrane
A, C, D, E, F A, C, D, E, F, G, H	Beta-lactamase	organic acid binding binding ion 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 organic acid binding binding ion 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	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR058218	Beta-lactamase OXA-48-like	Family
B	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
B	IPR001460	Penicillin-binding protein, transpeptidase	Domain
B	IPR002137	Beta-lactamase, class-D active site	Active Site
B	IPR050515	Class D beta-lactamase/transpeptidase	Family
A, C, D, E, F A, C, D, E, F, G, H	IPR058218	Beta-lactamase OXA-48-like	Family
A, C, D, E, F A, C, D, E, F, G, H	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, C, D, E, F A, C, D, E, F, G, H	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, C, D, E, F A, C, D, E, F, G, H	IPR002137	Beta-lactamase, class-D active site	Active Site
A, C, D, E, F A, C, D, E, F, G, H	IPR050515	Class D beta-lactamase/transpeptidase	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.