5E9V | pdb_00005e9v

Crystal structure of BRD9 bromodomain in complex with an indolizine ligand

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	d5e9vb_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5e9va_	All alpha proteins	Bromodomain-like	Bromodomain	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)
B	SCOP2B Superfamily	Bromodomain	8084285	3001843	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bromodomain	8084285	3001843	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	P53_tetramer	e5e9vB1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: P53_tetramer	ECOD (v294.1)
A	P53_tetramer	e5e9vA1	A: a/b three-layered sandwiches	X: beta-clip	H: p53 tetramerization domain	T: p53 tetramerization domain	F: P53_tetramer	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00439	Bromodomain (Bromodomain)	Bromodomain	Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Bromodomain-containing protein 9	binding nucleic acid binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process cellular response to stimulus double-strand break repair response to stimulus DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process cellular response to stress DNA damage response response to stress recombinational repair metabolic process macromolecule metabolic process double-strand break repair via homologous recombination DNA repair developmental process multicellular organismal process regulation of developmental process regulation of stem cell population maintenance stem cell population maintenance positive regulation of developmental process positive regulation of stem cell population maintenance positive regulation of multicellular organismal process regulation of multicellular organismal process maintenance of cell number RNA metabolic process regulation of primary 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 regulation of biosynthetic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process cellular developmental process negative regulation of developmental process negative regulation of biological process regulation of cell differentiation cell differentiation negative regulation of cellular process negative regulation of cell differentiation cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex GBAF complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane-bounded organelle ATPase complex protein-containing complex intracellular anatomical structure catalytic complex GBAF complex nucleus nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure organelle membraneless organelle SWI/SNF superfamily-type complex SWI/SNF complex site of double-strand break site of DNA damage membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR021900	Protein of unknown function DUF3512	Family
A, B	IPR001487	Bromodomain	Domain
A, B	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B	IPR051831	Bromodomain-containing	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9H8M2	Sezary syndrome

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.