6G88 | pdb_00006g88

Crystal structure of Enterococcus Faecium D63r Penicillin-Binding protein 5 (PBP5fm)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PBP_dimer	e6g88A1	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
A	Transpeptidase_1st	e6g88A2	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	MecA_N	e6g88A5	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: MecA_N	ECOD (1.6)
A	EUF08385	e6g88A3	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: EUF08385	ECOD (1.6)
A	Transpeptidase_2nd	e6g88A4	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	ECOD (1.6)
C	PBP_dimer	e6g88C3	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
C	Transpeptidase_1st	e6g88C1	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	MecA_N	e6g88C4	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: MecA_N	ECOD (1.6)
C	EUF08385	e6g88C5	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: EUF08385	ECOD (1.6)
C	Transpeptidase_2nd	e6g88C2	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	ECOD (1.6)
B	PBP_dimer	e6g88B3	A: beta complex topology	X: Penicillin binding protein dimerisation domain (From Topology)	H: Penicillin binding protein dimerisation domain (From Topology)	T: Penicillin binding protein dimerisation domain	F: PBP_dimer	ECOD (1.6)
B	Transpeptidase_1st	e6g88B5	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	MecA_N	e6g88B1	A: a+b two layers	X: Cystatin-like	H: NTF2-like (From Topology)	T: NTF2-like	F: MecA_N	ECOD (1.6)
B	EUF08385	e6g88B2	A: a+b two layers	X: ClpS-like	H: Penicillin binding protein ClpS-like domain (From Topology)	T: Penicillin binding protein ClpS-like domain	F: EUF08385	ECOD (1.6)
B	Transpeptidase_2nd	e6g88B4	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	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (utative)
C	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (utative)
B	3.10.450.100	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Low affinity penicillin-binding protein 5 (PBP5)	serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity organic acid binding binding ion binding serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity peptidoglycan L,D-transpeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase 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	cellular component organization cell wall organization or biogenesis cell wall organization cellular process 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	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
A, B, C	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C	IPR005311	Penicillin-binding protein, dimerisation domain	Domain
A, B, C	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B, C	IPR007887	Penicillin-binding protein 3-like, N-terminal domain	Domain
A, B, C	IPR050515	Class D beta-lactamase/transpeptidase	Family
A, B, C	IPR036138	Penicillin-binding protein, dimerisation domain superfamily	Homologous Superfamily

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.