4IEF

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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
B	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)
F	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	E set domains	8055053	3000070	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Caspase-like	8044003	3001096	SCOP2B (2022-06-29)
H	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)
A	Propeptide_C25	e4iefA1	A: beta sandwiches	X: Agglutinin HPA-like	H: Agglutinin HPA-like (From Topology)	T: Agglutinin HPA-like	F: Propeptide_C25	ECOD (1.6)
C	Propeptide_C25	e4iefC1	A: beta sandwiches	X: Agglutinin HPA-like	H: Agglutinin HPA-like (From Topology)	T: Agglutinin HPA-like	F: Propeptide_C25	ECOD (1.6)
E	Propeptide_C25	e4iefE1	A: beta sandwiches	X: Agglutinin HPA-like	H: Agglutinin HPA-like (From Topology)	T: Agglutinin HPA-like	F: Propeptide_C25	ECOD (1.6)
G	Propeptide_C25	e4iefG1	A: beta sandwiches	X: Agglutinin HPA-like	H: Agglutinin HPA-like (From Topology)	T: Agglutinin HPA-like	F: Propeptide_C25	ECOD (1.6)
B	Peptidase_C25_C	e4iefB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C25_C	ECOD (1.6)
B	Peptidase_C25_cat	e4iefB2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C25_cat	ECOD (1.6)
B	Peptidase_C25_N	e4iefB3	A: a/b three-layered sandwiches	X: Gingipain R extra N-terminal alpha/beta domain (From Topology)	H: Gingipain R extra N-terminal alpha/beta domain (From Topology)	T: Gingipain R extra N-terminal alpha/beta domain	F: Peptidase_C25_N	ECOD (1.6)
D	Peptidase_C25_C	e4iefD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C25_C	ECOD (1.6)
D	Peptidase_C25_cat	e4iefD2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C25_cat	ECOD (1.6)
D	Peptidase_C25_N	e4iefD3	A: a/b three-layered sandwiches	X: Gingipain R extra N-terminal alpha/beta domain (From Topology)	H: Gingipain R extra N-terminal alpha/beta domain (From Topology)	T: Gingipain R extra N-terminal alpha/beta domain	F: Peptidase_C25_N	ECOD (1.6)
F	Peptidase_C25_C	e4iefF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C25_C	ECOD (1.6)
F	Peptidase_C25_cat	e4iefF2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C25_cat	ECOD (1.6)
F	Peptidase_C25_N	e4iefF3	A: a/b three-layered sandwiches	X: Gingipain R extra N-terminal alpha/beta domain (From Topology)	H: Gingipain R extra N-terminal alpha/beta domain (From Topology)	T: Gingipain R extra N-terminal alpha/beta domain	F: Peptidase_C25_N	ECOD (1.6)
H	Peptidase_C25_C	e4iefH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Peptidase_C25_C	ECOD (1.6)
H	Peptidase_C25_cat	e4iefH2	A: a/b three-layered sandwiches	X: Caspase-like (From Topology)	H: Caspase-like (From Topology)	T: Caspase-like	F: Peptidase_C25_cat	ECOD (1.6)
H	Peptidase_C25_N	e4iefH3	A: a/b three-layered sandwiches	X: Gingipain R extra N-terminal alpha/beta domain (From Topology)	H: Gingipain R extra N-terminal alpha/beta domain (From Topology)	T: Gingipain R extra N-terminal alpha/beta domain	F: Peptidase_C25_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	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)
E	2.60.40.3800	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
G	2.60.40.3800	Mainly Beta	Sandwich	Immunoglobulin-like		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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF08126	Propeptide_C25 (Propeptide_C25)	Propeptide_C25	-	Family
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
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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity
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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR026444	Secretion system C-terminal sorting domain	Domain
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	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
B, D, F, H	IPR026444	Secretion system C-terminal sorting domain	Domain
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	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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4IEF

Complex of Porphyromonas gingivalis RgpB pro- and mature domains

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Protein Modification Annotation