1J35 | pdb_00001j35

Crystal Structure of Ca(II)-bound Gla Domain of Factor IX Complexed with Binding Protein

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)
A	d1j35a_	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	Snake coagglutinin alpha chain	(Protobothrops flavoviridis ) [TaxId: 88087 ],	SCOPe (2.08)
B	d1j35b_	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	C-type lectin domain	Snake coagglutinin beta chain	(Protobothrops flavoviridis ) [TaxId: 88087 ],	SCOPe (2.08)
C	d1j35c_	Small proteins	GLA-domain	GLA-domain	GLA-domain	Coagulation factor IX (IXa)	(Bos taurus ) [TaxId: 9913 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	C-type lectin-like	8032237	3001261	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8032239	3001261	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GLA-domain	8032238	3001028	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	Lectin_C	e1j35A1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: Lectin_C	ECOD (1.6)
B	Lectin_C	e1j35B1	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: C-type lectin-like	F: Lectin_C	ECOD (1.6)
C	Gla_1	e1j35C1	A: few secondary structure elements	X: GLA-domain (From Topology)	H: GLA-domain (From Topology)	T: GLA-domain	F: Gla_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)
B	3.10.100.10	Alpha Beta	Roll	Mannose-Binding Protein A	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain
B	PF00059	Lectin C-type domain (Lectin_C)	Lectin C-type domain	This family includes both long and short form C-type	Domain
C	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 IX-binding protein A chain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region
B	Coagulation factor IX-binding protein B chain	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding toxin activity	-	cellular anatomical structure extracellular region
C	Coagulation factor IX	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding calcium ion binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding calcium ion binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity endopeptidase activity serine hydrolase activity serine-type peptidase activity serine-type 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 proteolysis metabolic process cellular process 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 proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process zymogen activation gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle cellular anatomical structure organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001304	C-type lectin-like	Domain
A	IPR018378	C-type lectin, conserved site	Conserved Site
A	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
A	IPR050111	C-type lectin and snaclec domain-containing protein	Family
A	IPR016187	C-type lectin fold	Homologous Superfamily
B	IPR001304	C-type lectin-like	Domain
B	IPR018378	C-type lectin, conserved site	Conserved Site
B	IPR016186	C-type lectin-like/link domain superfamily	Homologous Superfamily
B	IPR050111	C-type lectin and snaclec domain-containing protein	Family
B	IPR016187	C-type lectin fold	Homologous Superfamily
C	IPR050442	Peptidase S1 family, coagulation factors	Family
C	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
C	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
C	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C	IPR001314	Peptidase S1A, chymotrypsin family	Family
C	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
C	IPR001254	Serine proteases, trypsin domain	Domain
C	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
C	IPR001881	EGF-like calcium-binding domain	Domain
C	IPR000742	EGF-like domain	Domain
C	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
C	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
C	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family