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
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F		e4df9F1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
E		e4df9E1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
D		e4df9D1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
C		e4df9C1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
B		e4df9B1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
A		e4df9A1	A: Alpha-beta plaits	X: Phage tail protein-like	H: Phage tail protein-like	T: DUF4488	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)
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)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.