6PT5 | pdb_00006pt5

Crystal Structure of Class D Beta-lactamase OXA-48 with Cefoxitin

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6pt5d1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
D	d6pt5d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
C	d6pt5c1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
C	d6pt5c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
B	d6pt5b1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
B	d6pt5b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
A	d6pt5a1	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
A	d6pt5a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-lactamase/transpeptidase-like	8074295	3001604	SCOP2B (2022-06-29)
B	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)
D	Transpeptidase_1st	e6pt5D1	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	Transpeptidase_2nd_1	e6pt5D2	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	Transpeptidase_1st	e6pt5C2	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	Transpeptidase_2nd_1	e6pt5C1	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	Transpeptidase_1st	e6pt5B1	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	Transpeptidase_2nd_1	e6pt5B2	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)
A	Transpeptidase_1st	e6pt5A2	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	Transpeptidase_2nd_1	e6pt5A1	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, B, C, D	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)
A, B, C, D	ARO:3007721	OXA-48-like beta-lactamase	carbapenem, penicillin beta-lactam	antibiotic inactivation	CARD (4.0.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, B, C, D	Class D Carbapenemase OXA-48	amide binding 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 amide binding 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
A, B, C, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B, C, D	IPR002137	Beta-lactamase, class-D active site	Active Site
A, B, C, D	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.