3JTC | pdb_00003jtc

Importance of Mg2+ in the Ca2+-Dependent Folding of the gamma-Carboxyglutamic Acid Domains of Vitamin K-Dependent clotting and anticlotting Proteins

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
Pharos: Disease Associations
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d3jtcc_	Small proteins	GLA-domain	GLA-domain	GLA-domain	Coagulation factor XIV (Protein C)	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3jtcd_	Small proteins	GLA-domain	GLA-domain	GLA-domain	Coagulation factor XIV (Protein C)	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3jtca_	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3jtcb_	Alpha and beta proteins (a+b)	MHC antigen-recognition domain	MHC antigen-recognition domain	MHC antigen-recognition domain	automated matches	(Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	GLA-domain	8041437	3001028	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GLA-domain	8041437	3001028	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MHC antigen-recognition domain	8041433	3000521	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MHC antigen-recognition domain	8041433	3000521	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)
C	PA14	e3jtcC1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: N-terminal beta-sandwich domain in anthrax protective antigen	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: PA14	ECOD (v294.1)
D	PDZ	e3jtcD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PDZ	ECOD (v294.1)
A	Cons_hypoth95	e3jtcA1	A: a/b three-layered sandwiches	X: N-terminal beta-sandwich domain in anthrax protective antigen	H: N-terminal beta-sandwich domain in anthrax protective antigen	T: N-terminal beta-sandwich domain in anthrax protective antigen	F: Cons_hypoth95	ECOD (v294.1)
B	PDZ	e3jtcB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: PDZ	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)
B	3.30.500.10	Alpha Beta	2-Layer Sandwich	Murine Class I Major Histocompatibility Complex, H2-DB	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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
C, D	Vitamin K-dependent protein C	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 regulation of biological process regulation of cellular process negative regulation of programmed cell death 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 regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of response to wounding regulation of coagulation regulation of multicellular organismal process regulation of hemostasis negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation negative regulation of response to wounding negative regulation of hemostasis negative regulation of coagulation regulation of wound healing negative regulation of multicellular organismal process regulation of establishment of endothelial barrier cellular developmental process regulation of developmental process positive regulation of endothelial cell development endothelium development positive regulation of biological process cell development regulation of cell differentiation epithelial cell differentiation regulation of cell development regulation of epithelial cell differentiation endothelial cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation cell differentiation regulation of endothelial cell development anatomical structure development positive regulation of cellular process developmental process epithelium development regulation of multicellular organismal development endothelial cell differentiation regulation of endothelial cell differentiation positive regulation of cell development positive regulation of establishment of endothelial barrier tissue development epithelial cell development establishment of endothelial barrier proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region extracellular space
A, B	Endothelial protein C receptor	molecular transducer activity signaling receptor 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 regulation of biological process negative regulation of coagulation negative regulation of biological 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 regulation of biological process negative regulation of coagulation negative regulation of biological process regulation of multicellular organismal process negative regulation of multicellular organismal process regulation of coagulation	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular organelle centrosome microtubule organizing center intracellular anatomical structure cytoskeleton membraneless organelle intracellular membraneless organelle microtubule cytoskeleton cell surface perinuclear region of cytoplasm cytoplasm cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
C, D	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C, D	IPR000742	EGF-like domain	Domain
C, D	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
C, D	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
C, D	IPR050442	Peptidase S1 family, coagulation factors	Family
C, D	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C, D	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
C, D	IPR001314	Peptidase S1A, chymotrypsin family	Family
C, D	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
C, D	IPR001254	Serine proteases, trypsin domain	Domain
C, D	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
C, D	IPR001881	EGF-like calcium-binding domain	Domain
C, D	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
C, D	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
A, B	IPR037055	MHC class I-like antigen recognition-like superfamily	Homologous Superfamily
A, B	IPR015669	Endothelial protein C receptor	Family
A, B	IPR011161	MHC class I-like antigen recognition-like	Domain
A, B	IPR011162	MHC classes I/II-like antigen recognition protein	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P04070	thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia thrombophilia due to protein C deficiency, autosomal recessive purpura fulminans Venous Thrombosis disseminated intravascular coagulation hereditary thrombophilia due to congenital protein C deficiency thrombophilia due to protein C deficiency, autosomal dominant venous thromboembolism arteritis hypertensive disorder thrombophilia pancreatic intraductal papillary-mucinous carcinoma thrombotic disease chronic kidney disease lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ovarian cancer
A, B	Pharos: Q9UNN8	coronary artery disease ulcerative colitis Liver Cirrhosis, Experimental astrocytic tumor gastric carcinoma invasive ductal breast carcinoma melanoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor cystic fibrosis heart disease oligodendroglioma skin basal cell carcinoma vascular disease ductal breast carcinoma in situ coronary artery disease ulcerative colitis Liver Cirrhosis, Experimental astrocytic tumor gastric carcinoma invasive ductal breast carcinoma melanoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor cystic fibrosis heart disease oligodendroglioma skin basal cell carcinoma vascular disease ductal breast carcinoma in situ malignant mesothelioma ovarian cancer thrombotic disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	CGU	Parent Component: GLU RESID: AA0032 PSI-MOD : L-gamma-carboxyglutamic acid MOD:00041

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.