4HPK

Crystal structure of Clostridium histolyticum colg collagenase collagen-binding domain 3B at 1.35 Angstrom resolution in presence of calcium nitrate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4hpka_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Collagen-binding domain	Class 1 collagenase	(Hathewaya histolytica ) [TaxId: 1498 ],	SCOPe (2.08)
B	d4hpkb_	All beta proteins	Galactose-binding domain-like	Galactose-binding domain-like	Collagen-binding domain	Class 1 collagenase	(Hathewaya histolytica ) [TaxId: 1498 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Collagen-binding domain	8033505	3001796	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Collagen-binding domain	8033505	3001796	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	PPC	e4hpkA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PPC	ECOD (1.6)
B	PPC	e4hpkB1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PPC	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.380	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.380	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04151	Bacterial pre-peptidase C-terminal domain (PPC)	Bacterial pre-peptidase C-terminal domain	This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (Pfam:PF00801) domain, which also are found in this context. ...	This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (Pfam:PF00801) domain, which also are found in this context. Visual analysis suggests that PKD and PPC are distantly related (personal obs:Bateman A, Yeats C).	Domain
B	PF04151	Bacterial pre-peptidase C-terminal domain (PPC)	Bacterial pre-peptidase C-terminal domain	This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (Pfam:PF00801) domain, which also are found in this context. ...	This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (Pfam:PF00801) domain, which also are found in this context. Visual analysis suggests that PKD and PPC are distantly related (personal obs:Bateman A, Yeats C).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Collagenase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity metalloendopeptidase activity metallopeptidase activity transition metal ion binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity metalloendopeptidase activity metallopeptidase activity transition metal ion binding zinc ion binding tripeptidase activity exopeptidase activity collagen binding protein-containing complex binding	collagen metabolic process metabolic process proteolysis primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region cellular anatomical entity
B	Collagenase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity metalloendopeptidase activity metallopeptidase activity transition metal ion binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity metalloendopeptidase activity metallopeptidase activity transition metal ion binding zinc ion binding tripeptidase activity exopeptidase activity collagen binding protein-containing complex binding	collagen metabolic process metabolic process proteolysis 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	IPR022409	PKD/Chitinase domain	Domain
A	IPR000601	PKD domain	Domain
A	IPR013661	Peptidase M9, collagenase, N-terminal domain	Domain
A	IPR035986	PKD domain superfamily	Homologous Superfamily
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR041379	Collagenase ColG-like, catalytic helper subdomain	Domain
A	IPR007280	Peptidase, C-terminal, archaeal/bacterial	Domain
A	IPR002169	Peptidase M9A/M9B, collagenase, bacterial	Family
B	IPR022409	PKD/Chitinase domain	Domain
B	IPR000601	PKD domain	Domain
B	IPR013661	Peptidase M9, collagenase, N-terminal domain	Domain
B	IPR035986	PKD domain superfamily	Homologous Superfamily
B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B	IPR041379	Collagenase ColG-like, catalytic helper subdomain	Domain
B	IPR007280	Peptidase, C-terminal, archaeal/bacterial	Domain
B	IPR002169	Peptidase M9A/M9B, collagenase, bacterial	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.