4DF9 | pdb_00004df9

Crystal structure of a putative peptidase (BF3526) from Bacteroides fragilis NCTC 9343 at 2.17 A resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	SCOP2B Superfamily	IgA peptidase N-terminal domain-like	8053830	3002233	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8053827	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8053827	3001975	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	IgA peptidase N-terminal domain-like	8053830	3002233	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8053827	3001975	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	IgA peptidase N-terminal domain-like	8053830	3002233	SCOP2B (2022-06-29)
D	SCOP2 Family	IgA peptidase-like	8044941	4004215	SCOP2 (2022-06-29)
D	SCOP2 Family	IgA peptidase N-terminal domain-like	8045124	4004305	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Metalloproteases (zincins), catalytic domain	8053827	3001975	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	IgA peptidase N-terminal domain-like	8053830	3002233	SCOP2 (2022-06-29)
E	SCOP2B Superfamily	IgA peptidase N-terminal domain-like	8053830	3002233	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8053827	3001975	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	IgA peptidase N-terminal domain-like	8053830	3002233	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Metalloproteases (zincins), catalytic domain	8053827	3001975	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	M64_N	e4df9A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: N-terminal domain in metallo-endopeptidase BACOVA_00663 (From Topology)	T: N-terminal domain in metallo-endopeptidase BACOVA_00663	F: M64_N	ECOD (1.6)
A	Peptidase_M64	e4df9A1	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M64	ECOD (1.6)
B	M64_N	e4df9B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: N-terminal domain in metallo-endopeptidase BACOVA_00663 (From Topology)	T: N-terminal domain in metallo-endopeptidase BACOVA_00663	F: M64_N	ECOD (1.6)
B	Peptidase_M64	e4df9B2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M64	ECOD (1.6)
C	M64_N	e4df9C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: N-terminal domain in metallo-endopeptidase BACOVA_00663 (From Topology)	T: N-terminal domain in metallo-endopeptidase BACOVA_00663	F: M64_N	ECOD (1.6)
C	Peptidase_M64	e4df9C2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M64	ECOD (1.6)
D	M64_N	e4df9D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: N-terminal domain in metallo-endopeptidase BACOVA_00663 (From Topology)	T: N-terminal domain in metallo-endopeptidase BACOVA_00663	F: M64_N	ECOD (1.6)
D	Peptidase_M64	e4df9D2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M64	ECOD (1.6)
E	M64_N	e4df9E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: N-terminal domain in metallo-endopeptidase BACOVA_00663 (From Topology)	T: N-terminal domain in metallo-endopeptidase BACOVA_00663	F: M64_N	ECOD (1.6)
E	Peptidase_M64	e4df9E2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M64	ECOD (1.6)
F	M64_N	e4df9F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: N-terminal domain in metallo-endopeptidase BACOVA_00663 (From Topology)	T: N-terminal domain in metallo-endopeptidase BACOVA_00663	F: M64_N	ECOD (1.6)
F	Peptidase_M64	e4df9F2	A: mixed a+b and a/b	X: Zincin-like	H: Metalloproteases (zincins) catalytic domain (From Topology)	T: Metalloproteases (zincins) catalytic domain	F: Peptidase_M64	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.3250	Mainly Beta	Sandwich	Immunoglobulin-like	Peptidase M64, N-terminal domain	CATH (4.3.0)
A	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
B	2.60.40.3250	Mainly Beta	Sandwich	Immunoglobulin-like	Peptidase M64, N-terminal domain	CATH (4.3.0)
B	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
C	2.60.40.3250	Mainly Beta	Sandwich	Immunoglobulin-like	Peptidase M64, N-terminal domain	CATH (4.3.0)
C	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
D	2.60.40.3250	Mainly Beta	Sandwich	Immunoglobulin-like	Peptidase M64, N-terminal domain	CATH (4.3.0)
D	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
E	2.60.40.3250	Mainly Beta	Sandwich	Immunoglobulin-like	Peptidase M64, N-terminal domain	CATH (4.3.0)
E	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)
F	2.60.40.3250	Mainly Beta	Sandwich	Immunoglobulin-like	Peptidase M64, N-terminal domain	CATH (4.3.0)
F	3.40.390.10	Alpha Beta	3-Layer(aba) Sandwich	Collagenase (Catalytic Domain)	Collagenase (Catalytic Domain)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF09471	IgA Peptidase M64 (Peptidase_M64)	IgA Peptidase M64	-	Family
A, B, C, D, E A, B, C, D, E, F	PF16217	Peptidase M64 N-terminus (M64_N)	Peptidase M64 N-terminus	This domain is found at the N-terminus of IgA Peptidase M64. Its function is unknown.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	putative peptidase	peptidase activity catalytic activity, acting on a protein metallopeptidase activity hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR038171	Peptidase M64, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR024079	Metallopeptidase, catalytic domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR032625	Peptidase M64, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR019026	Peptidase M64, IgA	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.