1CCF

How an Epidermal Growth Factor (EGF)-Like Domain Binds Calcium-High Resolution NMR Structure of the Calcium Form of the NH2-Terminal EGF-Like Domain in Coagulation Factor X

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d1ccfa_	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Factor X, N-terminal module	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	hEGF	e1ccfA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: hEGF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00008	EGF-like domain (EGF)	EGF-like domain	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is t ...	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.	Domain
A	PF00594	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain (Gla)	Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain	This domain is responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	COAGULATION FACTOR X	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding organic substance metabolic process organonitrogen compound metabolic process proteolysis multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	extracellular region extracellular space cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
A	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A	IPR001314	Peptidase S1A, chymotrypsin family	Family
A	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A	IPR001254	Serine proteases, trypsin domain	Domain
A	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR000742	EGF-like domain	Domain
A	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	BH2	Parent Component: ASP RESID: AA0027 PSI-MOD : (2S,3R)-3-hydroxyaspartic acid MOD:00036

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.