2GD4 | pdb_00002gd4

Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth C]	d2gd4c1	Multi-domain proteins (alpha and beta)	Serpins	Serpins	Serpins	Antithrombin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth I]	d2gd4i1	Multi-domain proteins (alpha and beta)	Serpins	Serpins	Serpins	Antithrombin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d2gd4b1	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Coagulation factor Xa, protease domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d2gd4h1	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Coagulation factor Xa, protease domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d2gd4a1	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Factor X, N-terminal module	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d2gd4l1	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Factor X, N-terminal module	human (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)
F [auth C]	SCOP2B Superfamily	Serpins	8037674	3001563	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Serpins	8037674	3001563	SCOP2B (2022-06-29)
E [auth B]	SCOP2B Superfamily	Trypsin-like serine proteases	8035341	3000114	SCOP2B (2022-06-29)
B [auth H]	SCOP2B Superfamily	Trypsin-like serine proteases	8035341	3000114	SCOP2B (2022-06-29)
D [auth A]	SCOP2B Superfamily	EGF/Laminin-like	8035338	3000412	SCOP2B (2022-06-29)
A [auth L]	SCOP2B Superfamily	EGF/Laminin-like	8035338	3000412	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)
F [auth C]	Serpin	e2gd4C1	A: a+b complex topology	X: Serpins (From Topology)	H: Serpins (From Topology)	T: Serpins	F: Serpin	ECOD (1.6)
C [auth I]	Serpin	e2gd4I1	A: a+b complex topology	X: Serpins (From Topology)	H: Serpins (From Topology)	T: Serpins	F: Serpin	ECOD (1.6)
E [auth B]	Trypsin	e2gd4B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (1.6)
B [auth H]	Trypsin	e2gd4H1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin	ECOD (1.6)
D [auth A]	FXa_inhibition	e2gd4A1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: FXa_inhibition	ECOD (1.6)
A [auth L]	FXa_inhibition	e2gd4L1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: FXa_inhibition	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth C]	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (4.3.0)
F [auth C]	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (4.3.0)
C [auth I]	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (4.3.0)
C [auth I]	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (4.3.0)
E [auth B]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B [auth H]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
D [auth A]	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
A [auth L]	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
C [auth I], F [auth C]	PF00079	Serpin (serine protease inhibitor) (Serpin)	Serpin (serine protease inhibitor)	Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.	Domain
B [auth H], E [auth B]	PF00089	Trypsin (Trypsin)	Trypsin		Domain
A [auth L], D [auth A]	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth I], F [auth C]	Antithrombin-III	enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity protein binding binding enzyme binding protease binding heparin binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity protein binding binding enzyme binding protease binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding	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 response to external stimulus regulation of blood coagulation 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 response to external stimulus regulation of blood coagulation response to external stimulus regulation of coagulation regulation of response to wounding regulation of response to stimulus regulation of response to stress regulation of wound healing regulation of multicellular organismal process regulation of hemostasis	cellular anatomical structure extracellular region extracellular space blood microparticle membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle cellular anatomical structure extracellular region extracellular space blood microparticle membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular exosome extracellular vesicle extracellular organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix external encapsulating structure
B [auth H], E [auth B]	Coagulation factor, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain	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 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 phospholipid binding lipid binding	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 cellular response to stimulus positive regulation of cell communication regulation of 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region extracellular space
A [auth L], D [auth A]	Coagulation factor X, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain	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 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 phospholipid binding lipid binding	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 cellular response to stimulus positive regulation of cell communication regulation of 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 cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling positive regulation of locomotion regulation of cell motility positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen organelle cytoplasm endoplasmic reticulum lumen endoplasmic reticulum extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth I], F [auth C]	IPR023795	Serpin, conserved site	Conserved Site
C [auth I], F [auth C]	IPR000215	Serpin family	Family
C [auth I], F [auth C]	IPR033829	Antithrombin-III, serpin domain	Domain
C [auth I], F [auth C]	IPR023796	Serpin domain	Domain
C [auth I], F [auth C]	IPR042178	Serpin superfamily, domain 1	Homologous Superfamily
C [auth I], F [auth C]	IPR042185	Serpin superfamily, domain 2	Homologous Superfamily
C [auth I], F [auth C]	IPR036186	Serpin superfamily	Homologous Superfamily
B [auth H], E [auth B]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
B [auth H], E [auth B]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B [auth H], E [auth B]	IPR000742	EGF-like domain	Domain
B [auth H], E [auth B]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
B [auth H], E [auth B]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
B [auth H], E [auth B]	IPR050442	Peptidase S1 family, coagulation factors	Family
B [auth H], E [auth B]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
B [auth H], E [auth B]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
B [auth H], E [auth B]	IPR001314	Peptidase S1A, chymotrypsin family	Family
B [auth H], E [auth B]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
B [auth H], E [auth B]	IPR001254	Serine proteases, trypsin domain	Domain
B [auth H], E [auth B]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
B [auth H], E [auth B]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth H], E [auth B]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
B [auth H], E [auth B]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
A [auth L], D [auth A]	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
A [auth L], D [auth A]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A [auth L], D [auth A]	IPR000742	EGF-like domain	Domain
A [auth L], D [auth A]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth L], D [auth A]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A [auth L], D [auth A]	IPR050442	Peptidase S1 family, coagulation factors	Family
A [auth L], D [auth A]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth L], D [auth A]	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
A [auth L], D [auth A]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth L], D [auth A]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth L], D [auth A]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth L], D [auth A]	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
A [auth L], D [auth A]	IPR001881	EGF-like calcium-binding domain	Domain
A [auth L], D [auth A]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A [auth L], D [auth A]	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth I], F [auth C]	Pharos: P01008	antithrombin III deficiency nephrotic syndrome Venous Thrombosis intracranial thrombosis disseminated intravascular coagulation adult acute respiratory distress syndrome venous thromboembolism intracerebral hemorrhage acute coronary syndrome thrombotic disease acute liver failure malignant glioma cerebrovascular disorder thrombocytopenia hypertensive disorder antithrombin III deficiency nephrotic syndrome Venous Thrombosis intracranial thrombosis disseminated intravascular coagulation adult acute respiratory distress syndrome venous thromboembolism intracerebral hemorrhage acute coronary syndrome thrombotic disease acute liver failure malignant glioma cerebrovascular disorder thrombocytopenia hypertensive disorder blood coagulation disease coronary artery disease thrombophilia heart disease brain injury pulmonary embolism
B [auth H], E [auth B]	Pharos: P00742	congenital factor X deficiency atrial fibrillation factor X deficiency thrombotic disease Prevention of deep vein thrombosis pulmonary embolism blood coagulation disease pancreatic ductal adenocarcinoma lung adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis breast fibroadenoma ductal breast carcinoma in situ invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
A [auth L], D [auth A]	Pharos: P00742	congenital factor X deficiency atrial fibrillation factor X deficiency thrombotic disease Prevention of deep vein thrombosis pulmonary embolism blood coagulation disease pancreatic ductal adenocarcinoma lung adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm psoriasis breast fibroadenoma ductal breast carcinoma in situ invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia