4YYK | pdb_00004yyk

Crystal structure of BRD9 Bromodomain bound to a crotonyllysine peptide

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Bromodomain	8084285	3001843	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bromodomain	8084285	3001843	SCOP2B (2022-06-29)
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)
E	ATP-synt_VA_C	e4yykE1	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
D	ATP-synt_VA_C	e4yykD1	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
B	ATP-synt_VA_C	e4yykB1	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)
A	ATP-synt_VA_C	e4yykA1	A: alpha bundles	X: Cytidine deaminase-like	H: KorB C-terminal domain	T: KorB C-terminal domain	F: ATP-synt_VA_C	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
D	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
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, D, E	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
C, F	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity RNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex organization cellular component biogenesis cellular component assembly chromatin organization protein-containing complex assembly chromatin remodeling cellular process cellular component organization or biogenesis nucleosome assembly nucleosome organization organelle organization telomere organization chromosome organization localization protein localization to chromatin protein localization to chromosome protein localization to chromosome, centromeric region protein localization to organelle macromolecule localization protein localization to CENP-A containing chromatin intracellular protein localization multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process regulation of megakaryocyte differentiation negative regulation of biological process cell development megakaryocyte differentiation regulation of cell differentiation regulation of cell development multicellular organism development negative regulation of megakaryocyte differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process developmental process regulation of biological process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation biological regulation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis	cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin cellular anatomical structure membrane extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure CENP-A containing chromatin protein-DNA complex intracellular membraneless organelle nucleosome chromosome chromatin chromosomal region intracellular organelle chromosome, centromeric core domain CENP-A containing nucleosome membraneless organelle chromosome, centromeric region chromosome, telomeric region nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, B, D, E	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
C, F	IPR009072	Histone-fold	Homologous Superfamily
C, F	IPR035425	CENP-T/Histone H4, histone fold	Domain
C, F	IPR001951	Histone H4	Family
C, F	IPR019809	Histone H4, conserved site	Conserved Site
C, F	IPR004823	TATA box binding protein associated factor (TAF), histone-like fold domain	Domain
A, B, D, E	IPR021900	Protein of unknown function DUF3512	Family
A, B, D, E	IPR001487	Bromodomain	Domain
A, B, D, E	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B, D, E	IPR051831	Bromodomain-containing	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: P62805	lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis lung carcinoma Malignant neoplasm of breast non-small cell lung carcinoma Pick disease squamous cell lung carcinoma acute myeloid leukemia atypical teratoid rhabdoid tumor breast carcinoma ductal breast carcinoma in situ exocrine pancreatic carcinoma hepatocellular carcinoma lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pilocytic astrocytoma ulcerative colitis allergic rhinitis autism spectrum disorder cystic fibrosis endogenous depression glioblastoma hypertensive disorder lung cancer malignant mesothelioma multiple sclerosis osteosarcoma psoriasis astrocytic tumor breast cancer diabetes mellitus endometriosis gout invasive ductal breast carcinoma
A, B, D, E	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.