5NDD | pdb_00005ndd

Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in complex with AZ8838 at 2.8 angstrom resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Class A (rhodopsin) G protein-coupled receptor-like	8091227	4001858	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	G protein-coupled receptor-like	8091228	3000473	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Lysozyme-like	8033861	3001879	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cytochromes	8057879	3001526	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	7tm_1_1	e5nddA1	A: alpha bundles	X: Family A G protein-coupled receptor-like (From Topology)	H: Family A G protein-coupled receptor-like (From Topology)	T: Family A G protein-coupled receptor-like	F: 7tm_1_1	ECOD (1.6)
A	7tm_1_1,Cytochrom_B562_1	e5nddA3	A: alpha bundles	X: Four-helical up-and-down bundle	H: Cytochromes (From Topology)	T: Cytochromes	F: 7tm_1_1,Cytochrom_B562_1	ECOD (1.6)
A	Phage_lysozyme_2	e5nddA2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07361	Cytochrome b562 (Cytochrom_B562)	Cytochrome b562	-	Family
A	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GC ...	This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Lysozyme,Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2	binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding protein binding G-protein alpha-subunit binding molecular transducer activity signaling receptor activity binding tetrapyrrole binding heme binding electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding small molecule binding protein binding G-protein alpha-subunit binding molecular transducer activity signaling receptor activity signaling receptor binding G protein-coupled receptor activity transmembrane signaling receptor activity enzyme binding protease binding peptide receptor activity thrombin-activated receptor activity proteinase-activated receptor activity G protein-coupled peptide receptor activity G-protein beta-subunit binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity	electron transport chain metabolic process cellular process generation of precursor metabolites and energy 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 electron transport chain metabolic process cellular process generation of precursor metabolites and energy 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 developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development mononuclear cell differentiation myeloid cell differentiation cell differentiation anatomical structure development dendritic cell differentiation mature conventional dendritic cell differentiation leukocyte differentiation regulation of biological process regulation of cellular process reactive oxygen species metabolic process positive regulation of biological process regulation of superoxide metabolic process positive regulation of reactive oxygen species metabolic process superoxide metabolic process positive regulation of metabolic process superoxide anion generation positive regulation of superoxide anion generation regulation of superoxide anion generation regulation of metabolic process regulation of reactive oxygen species metabolic process positive regulation of cellular process cellular response to stimulus regulation of signaling signaling regulation of JNK cascade regulation of signal transduction regulation of MAPK cascade intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus JNK cascade intracellular signaling cassette MAPK cascade regulation of cell communication signal transduction regulation of cellular component organization positive regulation of cellular component organization cell projection organization plasma membrane bounded cell projection assembly cellular component biogenesis cellular component organization pseudopodium assembly cellular component assembly positive regulation of cell projection organization cellular component organization or biogenesis plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis regulation of plasma membrane bounded cell projection assembly positive regulation of pseudopodium assembly regulation of pseudopodium assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly pseudopodium organization chemotaxis positive regulation of locomotion regulation of response to external stimulus response to external stimulus regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus taxis response to chemical regulation of locomotion locomotion biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus positive regulation of cell communication positive regulation of response to biotic stimulus positive regulation of signal transduction pattern recognition receptor signaling pathway immune response-activating signaling pathway positive regulation of toll-like receptor 3 signaling pathway positive regulation of immune response regulation of immune system process positive regulation of immune system process innate immune response-activating signaling pathway positive regulation of pattern recognition receptor signaling pathway regulation of innate immune response positive regulation of intracellular signal transduction regulation of pattern recognition receptor signaling pathway positive regulation of defense response regulation of immune response activation of innate immune response activation of immune response regulation of defense response cytoplasmic pattern recognition receptor signaling pathway regulation of response to biotic stimulus intracellular receptor signaling pathway regulation of cytoplasmic pattern recognition receptor signaling pathway endolysosomal toll-like receptor signaling pathway immune response-regulating signaling pathway regulation of response to stress regulation of toll-like receptor 3 signaling pathway positive regulation of innate immune response toll-like receptor 3 signaling pathway positive regulation of signaling regulation of biosynthetic process chemokine (C-X-C motif) ligand 2 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of chemokine production regulation of gene expression regulation of chemokine (C-X-C motif) ligand 2 production biosynthetic process regulation of cytokine production cytokine production chemokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal process macromolecule metabolic process negative regulation of biological process negative regulation of chemokine production negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cytokine production negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of multicellular organismal process interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process regulation of interleukin-1 production interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of interleukin-8 production interleukin-8 production regulation of interleukin-8 production positive regulation of JNK cascade positive regulation of MAPK cascade positive regulation of chemokine production system process renal system process regulation of renal system process regulation of blood pressure regulation of system process regulation of glomerular filtration positive regulation of glomerular filtration regulation of systemic arterial blood pressure circulatory system process renal system process involved in regulation of blood volume renal system process involved in regulation of systemic arterial blood pressure glomerular filtration blood circulation renal filtration negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction negative regulation of cell communication negative regulation of toll-like receptor 3 signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of immune system process interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production protein localization regulation of systemic arterial blood pressure by renin-angiotensin regulation of localization regulation of systemic arterial blood pressure by hormone establishment of protein localization nitrogen compound transport positive regulation of establishment of protein localization localization renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure cellular macromolecule localization establishment of protein localization to extracellular region regulation of systemic arterial blood pressure by circulatory renin-angiotensin protein secretion establishment of localization positive regulation of renin secretion into blood stream regulation of protein secretion regulation of secretion positive regulation of protein localization regulation of endocrine process renin secretion into blood stream cellular localization regulation of systemic arterial blood pressure mediated by a chemical signal regulation of protein localization transport positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell regulation of renin secretion into blood stream positive regulation of secretion signal release regulation of transport secretion regulation of establishment of protein localization export from cell cell-cell signaling regulation of protein transport positive regulation of protein secretion endocrine process positive regulation of transport protein transport regulation of cellular localization macromolecule localization cell activation lymphocyte activation cell activation involved in immune response leukocyte activation immune effector process T cell activation involved in immune response T cell activation leukocyte activation involved in immune response lymphocyte activation involved in immune response regulation of immune effector process regulation of myeloid leukocyte mediated immunity regulated exocytosis positive regulation of leukocyte mediated immunity leukocyte degranulation myeloid leukocyte mediated immunity vesicle-mediated transport myeloid leukocyte activation positive regulation of leukocyte degranulation positive regulation of regulated secretory pathway establishment of localization in cell leukocyte mediated immunity regulation of leukocyte mediated immunity exocytosis positive regulation of myeloid leukocyte mediated immunity eosinophil mediated immunity eosinophil activation positive regulation of exocytosis regulation of regulated secretory pathway regulation of eosinophil degranulation positive regulation of eosinophil degranulation eosinophil degranulation positive regulation of immune effector process eosinophil activation involved in immune response regulation of leukocyte degranulation regulation of vesicle-mediated transport myeloid cell activation involved in immune response regulation of exocytosis granulocyte activation defense response to virus response to virus positive regulation of DNA-templated transcription RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration cell migration cell motility cell chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration leukocyte migration cellular response to chemical stimulus leukocyte chemotaxis cell population proliferation leukocyte proliferation positive regulation of cytosolic calcium ion concentration positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction immune response-regulating cell surface receptor signaling pathway cell surface toll-like receptor signaling pathway immune response-activating cell surface receptor signaling pathway regulation of toll-like receptor 4 signaling pathway positive regulation of toll-like receptor 4 signaling pathway innate immune response activating cell surface receptor signaling pathway cell surface pattern recognition receptor signaling pathway cell surface receptor signaling pathway toll-like receptor 4 signaling pathway positive regulation of ERK1 and ERK2 cascade ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade import into cell positive regulation of membrane invagination positive regulation of endocytosis regulation of phagocytosis, engulfment membrane invagination phagocytosis plasma membrane invagination regulation of endocytosis membrane organization regulation of phagocytosis phagocytosis, engulfment positive regulation of phagocytosis positive regulation of phagocytosis, engulfment regulation of membrane invagination endocytosis positive regulation of organelle organization regulation of cytoskeleton organization regulation of actin filament-based process regulation of cellular component size protein-containing complex disassembly positive regulation of actin filament depolymerization regulation of protein-containing complex disassembly actin filament depolymerization regulation of actin filament depolymerization actin filament-based process positive regulation of protein-containing complex disassembly cellular component disassembly actin polymerization or depolymerization regulation of actin filament organization actin cytoskeleton organization protein-containing complex organization regulation of protein depolymerization positive regulation of protein depolymerization positive regulation of cytoskeleton organization actin filament organization regulation of actin polymerization or depolymerization positive regulation of supramolecular fiber organization regulation of organelle organization organelle organization regulation of actin filament length regulation of actin cytoskeleton organization regulation of supramolecular fiber organization supramolecular fiber organization protein depolymerization cytoskeleton organization regulation of anatomical structure size interleukin-6 production positive regulation of interleukin-6 production regulation of interleukin-6 production neutrophil-mediated killing of symbiont cell regulation of killing of cells of another organism disruption of cell in another organism regulation of programmed cell death positive regulation of neutrophil mediated cytotoxicity positive regulation of leukocyte mediated cytotoxicity response to bacterium positive regulation of neutrophil mediated killing of symbiont cell regulation of neutrophil mediated killing of gram-negative bacterium biological process involved in interaction with symbiont killing of cells of another organism positive regulation of programmed cell death leukocyte mediated cytotoxicity cell death positive regulation of neutrophil mediated killing of bacterium regulation of cell killing positive regulation of cell killing disruption of anatomical structure in another organism positive regulation of killing of cells of another organism positive regulation of neutrophil mediated killing of gram-negative bacterium defense response to Gram-negative bacterium biological process involved in symbiotic interaction regulation of neutrophil mediated killing of bacterium defense response to bacterium positive regulation of defense response to bacterium neutrophil mediated immunity modulation of process of another organism regulation of biological process involved in symbiotic interaction regulation of defense response to bacterium neutrophil-mediated killing of bacterium neutrophil mediated cytotoxicity regulation of neutrophil mediated cytotoxicity regulation of leukocyte mediated cytotoxicity regulation of neutrophil mediated killing of symbiont cell killing by host of symbiont cells neutrophil-mediated killing of gram-negative bacterium programmed cell death cell killing positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity neutrophil activation regulation of toll-like receptor 2 signaling pathway positive regulation of toll-like receptor 2 signaling pathway toll-like receptor 2 signaling pathway small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction Rho protein signal transduction regulation of Rho protein signal transduction positive regulation of Rho protein signal transduction positive regulation of small GTPase mediated signal transduction regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction negative regulation of protein transport negative regulation of transport negative regulation of secretion negative regulation of hormone secretion negative regulation of secretion by cell regulation of peptide hormone secretion negative regulation of peptide hormone secretion regulation of hormone levels negative regulation of establishment of protein localization negative regulation of protein secretion regulation of hormone secretion regulation of peptide secretion hormone secretion negative regulation of peptide secretion peptide secretion amide transport negative regulation of protein localization regulation of peptide transport peptide transport negative regulation of insulin secretion regulation of insulin secretion peptide hormone secretion hormone transport insulin secretion negative regulation of JNK cascade negative regulation of MAPK cascade regulation of tube diameter regulation of tube size vascular process in circulatory system blood vessel diameter maintenance vasodilation positive chemotaxis positive regulation of positive chemotaxis regulation of positive chemotaxis epithelium development endothelial cell differentiation endothelium development tissue development epithelial cell differentiation endothelial cell development epithelial cell development establishment of endothelial barrier cell junction maintenance cell junction organization cellular component maintenance cell-cell junction maintenance cell-cell junction organization inflammatory response G protein-coupled receptor signaling pathway regulation of blood coagulation regulation of coagulation regulation of response to wounding regulation of wound healing regulation of hemostasis cytokine production involved in immune response production of molecular mediator of immune response regulation of cytokine production involved in immune response positive regulation of cytokine production involved in immune response positive regulation of production of molecular mediator of immune response regulation of production of molecular mediator of immune response response to cytokine cytokine-mediated signaling pathway cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway negative regulation of tumor necrosis factor-mediated signaling pathway response to peptide regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus negative regulation of cytokine-mediated signaling pathway response to tumor necrosis factor regulation of type II interferon production type II interferon production positive regulation of type II interferon production carbohydrate derivative catabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process symbiont-mediated cytolysis of host cell viral life cycle cytolysis biological process involved in interaction with host viral release from host cell by cytolysis exit from host cell viral process cytolysis in another organism viral release from host cell symbiont-mediated killing of host cell cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process	cellular anatomical structure periplasmic space cell projection pseudopodium plasma membrane bounded cell projection membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cell periphery cellular anatomical structure periplasmic space cell projection pseudopodium plasma membrane bounded cell projection membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system cell periphery plasma membrane membrane early endosome endosome intracellular vesicle cytoplasmic vesicle vesicle host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR010980	Cytochrome c/b562	Homologous Superfamily
A	IPR009155	Cytochrome b562	Family
A	IPR002281	Protease-activated receptor 2	Family
A	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A	IPR003912	Protease-activated receptor	Family
A	IPR052619	Bacteriophage lysozyme-like	Family
A	IPR001165	T4-type lysozyme	Family
A	IPR034690	Endolysin T4 type	Family
A	IPR002196	Glycoside hydrolase, family 24	Family
A	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P55085	melanoma Pruritus gastroenteritis myocardial ischemia osteosarcoma pilocytic astrocytoma primitive neuroectodermal tumor astrocytic tumor ulcerative colitis coronary artery disease facioscapulohumeral muscular dystrophy hepatocellular carcinoma large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm melanoma Pruritus gastroenteritis myocardial ischemia osteosarcoma pilocytic astrocytoma primitive neuroectodermal tumor astrocytic tumor ulcerative colitis coronary artery disease facioscapulohumeral muscular dystrophy hepatocellular carcinoma large cell medulloblastoma malignant ependymoma malignant pancreatic neoplasm nephrosclerosis ovarian cancer pituitary cancer atypical teratoid rhabdoid tumor cutaneous melanoma lung adenocarcinoma malignant glioma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm polycystic ovary syndrome psoriasis breast cancer exocrine pancreatic carcinoma glioblastoma interstitial cystitis malignant colon neoplasm malignant mesothelioma

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Transmembrane	Alpha-helical polytopic	Rhodopsin-like receptors and pumps	G-protein coupled receptors, family A

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	Protease-activated receptor 2 (PAR2) with bound AZ8838

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.