4IEF | pdb_00004ief

Complex of Porphyromonas gingivalis RgpB pro- and mature domains

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d4iefh2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
H	d4iefh1	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Gingipain R (RgpB), N-terminal domain	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
H	d4iefh3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
F	d4ieff2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
F	d4ieff1	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Gingipain R (RgpB), N-terminal domain	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
F	d4ieff3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
D	d4iefd2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
D	d4iefd1	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Gingipain R (RgpB), N-terminal domain	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
D	d4iefd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
B	d4iefb2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
B	d4iefb1	Alpha and beta proteins (a/b)	Caspase-like	Caspase-like	Gingipain R (RgpB), N-terminal domain	automated matches	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)
B	d4iefb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Porphyromonas gingivalis W83 ) [TaxId: 242619 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	E set domains	8055053	3000070	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	E set domains	8055053	3000070	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	E set domains	8055053	3000070	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	E set domains	8055053	3000070	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)
H	Clenterotox	e4iefH1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Clenterotox	ECOD (v294.1)
H	Med26	e4iefH2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)
F	Clenterotox	e4iefF1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Clenterotox	ECOD (v294.1)
F	MPI_cupin_dom	e4iefF2	A: a/b three-layered sandwiches	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: MPI_cupin_dom	ECOD (v294.1)
D	HSP90,HATPase_c_3	e4iefD1	A: a/b three-layered sandwiches	X: LidA	H: LidA	T: LidA	F: HSP90,HATPase_c_3	ECOD (v294.1)
D	Med26	e4iefD2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)
B	Clenterotox	e4iefB1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: Clenterotox	ECOD (v294.1)
B	Med26	e4iefB2	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: Med26	ECOD (v294.1)
G	SmpA_OmlA	e4iefG1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
E	SmpA_OmlA	e4iefE1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)
C	Bunya_nucleocap	e4iefC1	A: a/b three-layered sandwiches	X: Leanyer virus nucleoprotein-related	H: Leanyer virus nucleoprotein-related	T: Leanyer virus nucleoprotein-related	F: Bunya_nucleocap	ECOD (v294.1)
A	SmpA_OmlA	e4iefA1	A: a/b three-layered sandwiches	X: beta-Grasp	H: HTH	T: winged helix domain	F: SmpA_OmlA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.50.10390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Gingipain r	CATH (4.3.0)
H	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
H	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	3.40.50.10390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Gingipain r	CATH (4.3.0)
F	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	3.40.50.10390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Gingipain r	CATH (4.3.0)
D	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.40.50.10390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Gingipain r	CATH (4.3.0)
B	3.40.50.1460	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G	2.60.40.3800	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
E	2.60.40.3800	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
C	2.60.40.3800	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.40.3800	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF03785	Peptidase family C25, C terminal ig-like domain (Peptidase_C25_C)	Peptidase family C25, C terminal ig-like domain		Domain
B, D, F, H	PF01364	Peptidase family C25 (Peptidase_C25)	Peptidase family C25		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Gingipain R2 Mature Domain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region
A, C, E, G	Gingipain R2 Pro-Domain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding cysteine-type peptidase activity peptidase activity calcium-dependent cysteine-type endopeptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
B, D, F, H	IPR039392	Gingipain, N-terminal	Domain
B, D, F, H	IPR005536	Peptidase C25, Ig-like domain	Domain
B, D, F, H	IPR012600	Gingipain propeptide	Domain
B, D, F, H	IPR038490	Gingipain propeptide superfamily	Homologous Superfamily
B, D, F, H	IPR026444	Secretion system, C-terminal sorting domain	Domain
B, D, F, H	IPR041333	Peptidase M60, C-terminal	Domain
B, D, F, H	IPR001769	Gingipain	Domain
B, D, F, H	IPR029031	Gingipain, N-terminal superfamily	Homologous Superfamily
B, D, F, H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D, F, H	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A, C, E, G	IPR029030	Caspase-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR039392	Gingipain, N-terminal	Domain
A, C, E, G	IPR005536	Peptidase C25, Ig-like domain	Domain
A, C, E, G	IPR012600	Gingipain propeptide	Domain
A, C, E, G	IPR038490	Gingipain propeptide superfamily	Homologous Superfamily
A, C, E, G	IPR026444	Secretion system, C-terminal sorting domain	Domain
A, C, E, G	IPR041333	Peptidase M60, C-terminal	Domain
A, C, E, G	IPR001769	Gingipain	Domain
A, C, E, G	IPR029031	Gingipain, N-terminal superfamily	Homologous Superfamily
A, C, E, G	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C, E, G	IPR014756	Immunoglobulin E-set	Homologous Superfamily