5ZKQ

Crystal structure of the human platelet-activating factor receptor in complex with ABT-491

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: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091182	3000473	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	G protein-coupled receptor-like	8091182	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091182	3000473	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	G protein-coupled receptor-like	8091182	3000473	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	7tm_1_1	e5zkqB1	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)
B	Phage_lysozyme_2	e5zkqB2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)
A	7tm_1_1	e5zkqA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A, B	PF00001	7 transmembrane receptor (rhodopsin family) (7tm_1)	7 transmembrane receptor (rhodopsin family)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Platelet-activating factor receptor,Endolysin,Endolysin,Platelet-activating factor receptor	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity binding lipid binding lipopolysaccharide binding carbohydrate derivative binding hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity molecular transducer activity G protein-coupled receptor activity transmembrane signaling receptor activity signaling receptor activity binding lipid binding lipopolysaccharide binding carbohydrate derivative binding platelet activating factor receptor activity phospholipid binding pattern recognition receptor activity lipopolysaccharide immune receptor activity protein binding kinase binding enzyme binding protein kinase binding mitogen-activated protein kinase binding G protein-coupled purinergic nucleotide receptor activity purinergic nucleotide receptor activity nucleotide receptor activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process macromolecule catabolic process glycosaminoglycan catabolic process organic substance metabolic process aminoglycan metabolic process peptidoglycan metabolic process nitrogen compound metabolic process metabolic process macromolecule metabolic process organic substance catabolic process symbiont-mediated cytolysis of host cell viral life cycle disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction viral release from host cell by cytolysis disruption of cellular anatomical structure in another organism exit from host cell viral process cytolysis in another organism cellular process viral release from host cell disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing disruption of plasma membrane integrity in another organism cell wall organization or biogenesis cell wall macromolecule catabolic process cell wall macromolecule metabolic process positive regulation of locomotion regulation of cell motility regulation of cellular process positive regulation of biological process positive regulation of cell migration positive regulation of cell motility regulation of cell migration cellular extravasation cell migration regulation of immune system process cell motility positive regulation of immune system process locomotion positive regulation of cellular process regulation of biological process regulation of leukocyte migration biological regulation positive regulation of leukocyte migration leukocyte migration immune system process regulation of locomotion positive regulation of cellular extravasation regulation of cellular extravasation immune response interleukin-6 production multicellular organismal process cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of interleukin-6 production regulation of interleukin-6 production positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production organic substance biosynthetic process cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process multi-multicellular organism process reproductive process parturition multi-organism reproductive process cellular response to stimulus cellular response to nitrogen compound response to organic substance response to organonitrogen compound response to endogenous stimulus response to organophosphorus cellular response to organic cyclic compound response to oxygen-containing compound response to nitrogen compound response to purine-containing compound response to cAMP cellular response to oxygen-containing compound cellular response to endogenous stimulus cellular response to chemical stimulus cellular response to organonitrogen compound response to chemical cellular response to cAMP cellular response to organic substance response to organic cyclic compound chemotaxis taxis positive regulation of protein metabolic process organonitrogen compound biosynthetic process positive regulation of translation regulation of primary metabolic process regulation of nitrogen compound metabolic process post-transcriptional regulation of gene expression protein metabolic process regulation of protein metabolic process primary metabolic process translation positive regulation of nitrogen compound metabolic process regulation of translation regulation of reproductive process multicellular organismal reproductive process positive regulation of maternal process involved in parturition maternal process involved in parturition regulation of maternal process involved in parturition positive regulation of reproductive process response to ketone response to lipid response to glucocorticoid response to corticosteroid response to hormone response to steroid hormone response to dexamethasone positive regulation of leukocyte cell-cell adhesion regulation of leukocyte adhesion to vascular endothelial cell leukocyte cell-cell adhesion leukocyte tethering or rolling positive regulation of cell-cell adhesion cell adhesion cell-cell adhesion positive regulation of leukocyte tethering or rolling regulation of cell-cell adhesion positive regulation of cell adhesion regulation of cell adhesion positive regulation of leukocyte adhesion to vascular endothelial cell regulation of leukocyte tethering or rolling leukocyte adhesion to vascular endothelial cell regulation of leukocyte cell-cell adhesion regulation of localization regulation of transcytosis transport regulation of transport positive regulation of transcytosis regulation of vesicle-mediated transport establishment of localization vesicle-mediated transport localization positive regulation of transport transcytosis response to symbiont response to symbiotic bacterium signaling phospholipase C-activating G protein-coupled receptor signaling pathway cell communication G protein-coupled receptor signaling pathway signal transduction cellular response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine response to 2-O-acetyl-1-O-hexadecyl-sn-glycero-3-phosphocholine cellular response to ether response to ether cellular response to lipid cell population proliferation regulation of smooth muscle cell proliferation positive regulation of cell population proliferation smooth muscle cell proliferation positive regulation of smooth muscle cell proliferation regulation of cell population proliferation muscle cell proliferation inflammatory response RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II heterocycle metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II cellular nitrogen compound metabolic process nucleobase-containing compound biosynthetic process heterocycle biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process aromatic compound biosynthetic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription cellular aromatic compound metabolic process response to fatty acid cellular response to fatty acid regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production polyol metabolic process small molecule biosynthetic process inositol trisphosphate biosynthetic process organic hydroxy compound metabolic process alcohol metabolic process inositol phosphate metabolic process organophosphate metabolic process organophosphate biosynthetic process inositol phosphate biosynthetic process organic hydroxy compound biosynthetic process phosphate-containing compound metabolic process polyol biosynthetic process alcohol biosynthetic process inositol trisphosphate metabolic process small molecule metabolic process phosphorus metabolic process regulation of immune effector process neutrophil activation regulation of myeloid leukocyte mediated immunity positive regulation of leukocyte mediated immunity regulated exocytosis cell activation involved in immune response leukocyte degranulation myeloid leukocyte mediated immunity myeloid leukocyte activation neutrophil activation involved in immune response positive regulation of leukocyte degranulation positive regulation of immune response positive regulation of regulated secretory pathway establishment of localization in cell leukocyte mediated immunity immune effector process regulation of secretion regulation of leukocyte mediated immunity exocytosis regulation of response to stimulus positive regulation of myeloid leukocyte mediated immunity regulation of immune response cellular localization positive regulation of secretion by cell positive regulation of exocytosis leukocyte activation positive regulation of response to stimulus regulation of regulated secretory pathway neutrophil mediated immunity secretion by cell regulation of secretion by cell positive regulation of secretion regulation of neutrophil degranulation leukocyte activation involved in immune response neutrophil degranulation positive regulation of immune effector process regulation of leukocyte degranulation secretion cell activation export from cell myeloid cell activation involved in immune response regulation of exocytosis positive regulation of neutrophil degranulation granulocyte activation regulation of inositol phosphate biosynthetic process positive regulation of phosphate metabolic process regulation of small molecule metabolic process regulation of phosphate metabolic process positive regulation of phosphorus metabolic process regulation of alcohol biosynthetic process carbohydrate biosynthetic process positive regulation of inositol phosphate biosynthetic process regulation of phosphorus metabolic process positive regulation of carbohydrate metabolic process regulation of carbohydrate metabolic process carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process positive regulation of alcohol biosynthetic process system process circulatory system process regulation of blood pressure regulation of biological quality negative regulation of blood pressure blood circulation gastro-intestinal system smooth muscle contraction positive regulation of smooth muscle contraction regulation of system process muscle contraction muscle system process regulation of muscle system process positive regulation of gastro-intestinal system smooth muscle contraction regulation of gastro-intestinal system smooth muscle contraction smooth muscle contraction regulation of smooth muscle contraction regulation of muscle contraction positive regulation of muscle contraction response to abiotic stimulus cellular response to gravity response to gravity cellular response to abiotic stimulus cellular response to environmental stimulus	host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane cell periphery plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001165	T4-type lysozyme	Family
A, B	IPR034690	Endolysin T4 type	Family
A, B	IPR002196	Glycoside hydrolase, family 24	Family
A, B	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A, B	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A, B	IPR000276	G protein-coupled receptor, rhodopsin-like	Family
A, B	IPR017452	GPCR, rhodopsin-like, 7TM	Domain
A, B	IPR002282	Platelet-activating factor receptor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P25105	polycystic ovary syndrome Liver Cirrhosis, Experimental amyotrophic lateral sclerosis facioscapulohumeral muscular dystrophy interstitial cystitis osteosarcoma psoriasis ulcerative colitis cystic fibrosis gastric carcinoma juvenile dermatomyositis malignant pancreatic neoplasm ovarian cancer exocrine pancreatic carcinoma hepatocellular carcinoma polycystic ovary syndrome Liver Cirrhosis, Experimental amyotrophic lateral sclerosis facioscapulohumeral muscular dystrophy interstitial cystitis osteosarcoma psoriasis ulcerative colitis cystic fibrosis gastric carcinoma juvenile dermatomyositis malignant pancreatic neoplasm ovarian cancer exocrine pancreatic carcinoma hepatocellular carcinoma large cell medulloblastoma MALT lymphoma tuberculosis

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	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, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	G Protein-Coupled Receptors: Class A	Platelet activating factor complex with bound antagonist SR 27417

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.