4DY0

Crystal structure of native protease nexin-1 with heparin

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)
A	d4dy0a_	Multi-domain proteins (alpha and beta)	Serpins	Serpins	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d4dy0b_	Multi-domain proteins (alpha and beta)	Serpins	Serpins	automated matches	automated matches	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)
A	SCOP2B Superfamily	Serpins	8070197	3001563	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Serpins	8070197	3001563	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	Serpin	e4dy0A1	A: a+b complex topology	X: Serpins (From Topology)	H: Serpins (From Topology)	T: Serpins	F: Serpin	ECOD (1.6)
B	Serpin	e4dy0B1	A: a+b complex topology	X: Serpins (From Topology)	H: Serpins (From Topology)	T: Serpins	F: Serpin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (4.3.0)
A	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (4.3.0)
B	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (4.3.0)
B	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glia-derived nexin	protein binding binding signaling receptor 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 glycosaminoglycan binding carbohydrate derivative binding protein binding binding signaling receptor 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 glycosaminoglycan binding carbohydrate derivative binding heparin binding sulfur compound binding	developmental process regulation of development, heterochronic regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation cell differentiation cellular process regulation of timing of cell differentiation multicellular organismal process epithelium development reproductive system development developmental process regulation of development, heterochronic regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation cell differentiation cellular process regulation of timing of cell differentiation multicellular organismal process epithelium development reproductive system development tube development reproductive process gland development animal organ development developmental process involved in reproduction tissue development multicellular organism development seminal vesicle development anatomical structure development reproductive structure development seminal vesicle epithelium development system development cerebellum morphogenesis cerebellar cortex morphogenesis head development hindbrain morphogenesis brain development cerebellar granular layer development nervous system development cerebellar cortex development cerebellar granular layer morphogenesis anatomical structure morphogenesis cerebellum development central nervous system development metencephalon development hindbrain development regulation of body fluid levels response to stimulus negative regulation of biological process regulation of cell activation negative regulation of cell adhesion negative regulation of platelet activation regulation of coagulation regulation of biological quality response to wounding negative regulation of homotypic cell-cell adhesion negative regulation of wound healing negative regulation of blood coagulation response to external stimulus blood coagulation negative regulation of hemostasis regulation of platelet activation regulation of response to stimulus negative regulation of response to external stimulus negative regulation of cell-cell adhesion regulation of wound healing negative regulation of multicellular organismal process platelet activation regulation of response to external stimulus homotypic cell-cell adhesion regulation of response to wounding cell adhesion cell-cell adhesion response to stress regulation of response to stress negative regulation of cellular process coagulation regulation of cell-cell adhesion regulation of multicellular organismal process regulation of hemostasis wound healing negative regulation of response to stimulus regulation of homotypic cell-cell adhesion regulation of cell adhesion regulation of blood coagulation hemostasis cell activation negative regulation of platelet aggregation negative regulation of response to wounding platelet aggregation negative regulation of cell activation regulation of platelet aggregation negative regulation of coagulation catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process regulation of growth regulation of cellular component organization growth negative regulation of cell growth regulation of cell growth cell growth cellular component organization negative regulation of growth cellular component organization or biogenesis negative regulation of proteolysis regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of primary metabolic process regulation of proteolysis proteolysis regulation of metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of localization transport regulation of transport regulation of monoatomic ion transport negative regulation of monoatomic ion transport negative regulation of transport regulation of sodium ion transport establishment of localization metal ion transport localization monoatomic ion transport negative regulation of sodium ion transport monoatomic cation transport regulation of metal ion transport sodium ion transport cellular response to stimulus negative regulation of signaling signaling regulation of signal transduction negative regulation of cell communication cell communication negative regulation of smoothened signaling pathway signal transduction regulation of smoothened signaling pathway regulation of signaling cell surface receptor signaling pathway negative regulation of signal transduction smoothened signaling pathway regulation of cell communication regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion secretion by cell secretion export from cell negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of protein maturation negative regulation of plasminogen activation negative regulation of protein maturation cellular biosynthetic process negative regulation of cellular metabolic process protein maturation regulation of plasminogen activation plasminogen activation regulation of biosynthetic process zymogen activation cellular metabolic process regulation of cellular metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing regulation of macromolecule biosynthetic process negative regulation of protein processing multi-multicellular organism process multicellular organismal reproductive process mating behavior behavior mating plug formation reproductive behavior insemination multi-organism reproductive process copulation negative regulation of catabolic process regulation of catabolic process negative regulation of protein catabolic process regulation of protein catabolic process trans-synaptic signaling modulation of chemical synaptic transmission synaptic transmission, glutamatergic cell-cell signaling regulation of synaptic transmission, glutamatergic chemical synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling nerve development innervation positive regulation of cell communication positive regulation of biological process long-term synaptic potentiation positive regulation of cellular process regulation of synaptic plasticity positive regulation of synaptic transmission positive regulation of signaling vesicle organization organelle organization secretory granule organization endomembrane system organization positive regulation of nervous system development astrocyte differentiation cell development regulation of neurogenesis regulation of gliogenesis regulation of astrocyte differentiation positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis gliogenesis positive regulation of cell differentiation positive regulation of neurogenesis positive regulation of astrocyte differentiation regulation of multicellular organismal development positive regulation of cell development regulation of glial cell differentiation positive regulation of glial cell differentiation glial cell differentiation positive regulation of multicellular organismal process detection of external stimulus system process nervous system process response to mechanical stimulus detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus response to abiotic stimulus detection of stimulus involved in sensory perception	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity intracellular anatomical structure cytoplasm cytosol neuromuscular junction synapse cell junction extracellular region membrane-bounded organelle intracellular vesicle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity intracellular anatomical structure cytoplasm cytosol neuromuscular junction synapse cell junction extracellular region membrane-bounded organelle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle secretory granule secretory vesicle platelet alpha granule vesicle extracellular vesicle extracellular organelle extracellular membrane-bounded organelle extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023795	Serpin, conserved site	Conserved Site
A, B	IPR000215	Serpin family	Family
A, B	IPR036186	Serpin superfamily	Homologous Superfamily
A, B	IPR023796	Serpin domain	Domain
A, B	IPR042178	Serpin superfamily, domain 1	Homologous Superfamily
A, B	IPR042185	Serpin superfamily, domain 2	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P07093	pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis acute myeloid leukemia cystic fibrosis gastric carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm ovarian cancer pterygium atypical teratoid rhabdoid tumor Duchenne muscular dystrophy interstitial cystitis lung cancer malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis acute myeloid leukemia cystic fibrosis gastric carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm ovarian cancer pterygium atypical teratoid rhabdoid tumor Duchenne muscular dystrophy interstitial cystitis lung cancer malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma Sjogren syndrome cutaneous lupus erythematosus ductal breast carcinoma in situ large cell medulloblastoma lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma

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.