5JB9 | pdb_00005jb9

Crystal structure of factor IXa K98T variant in complex with PPACK

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)
B [auth S]	d5jb9s_	All beta proteins	Trypsin-like serine proteases	Trypsin-like serine proteases	Eukaryotic proteases	Coagulation factor IXa, protease domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth E]	d5jb9e_	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Factor IX (IXa)	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)
B [auth S]	SCOP2B Superfamily	Trypsin-like serine proteases	8042263	3000114	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)
B [auth S]		e5jb9S1	A: Thymine dioxygenase JBP1 DNA-binding domain-like	X: Oligo-peptide binding protein (OPPA) insertion domain	H: Oligo-peptide binding protein (OPPA) insertion domain	T: DnaJ	F:	ECOD (20:10:01)
A [auth E]		e5jb9E1	A: Thymine dioxygenase JBP1 DNA-binding domain-like	X: Oligo-peptide binding protein (OPPA) insertion domain	H: Oligo-peptide binding protein (OPPA) insertion domain	T: DnaJ	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth S]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
A [auth E]	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
B [auth S]	PF00089	Trypsin (Trypsin)	Trypsin		Domain
A [auth E]	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
B [auth S]	Coagulation factor IX	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 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	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix external encapsulating structure intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen cytoplasm endoplasmic reticulum lumen endoplasmic reticulum
A [auth E]	Coagulation factor IX	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 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	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane extracellular matrix external encapsulating structure intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle organelle lumen cytoplasm endoplasmic reticulum lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth S]	Pharos: P00740	hemophilia B hemophilia A thrombophilia, X-linked, due to factor 9 defect coumarin resistance malignant mesothelioma thrombophilia thrombotic disease Autosomal Hemophilia A hemophilia bipolar disorder psoriasis vascular disease congenital factor XI deficiency
A [auth E]	Pharos: P00740	hemophilia B hemophilia A thrombophilia, X-linked, due to factor 9 defect coumarin resistance malignant mesothelioma thrombophilia thrombotic disease Autosomal Hemophilia A hemophilia bipolar disorder psoriasis vascular disease congenital factor XI deficiency