6G0S

Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated SIRT7 peptide (K272ac/K275ac)

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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Bromodomain	8084245	3001843	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Bromodomain	8084245	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)
A	Bromodomain	e6g0sA1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
C [auth B]	Bromodomain	e6g0sB1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
C [auth B]	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, C [auth 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, C [auth B]	Bromodomain-containing protein 4	p53 binding protein binding binding basal transcription machinery binding RNA polymerase binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding p53 binding protein binding binding basal transcription machinery binding RNA polymerase binding RNA polymerase II complex binding basal RNA polymerase II transcription machinery binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding transcription regulatory region nucleic acid binding transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding transcription coactivator activity histone reader activity chromatin-protein adaptor activity protein-containing complex binding P-TEFb complex binding protein serine/threonine kinase activity RNA polymerase II CTD heptapeptide repeat modifying activity catalytic activity, acting on a protein kinase activity protein kinase activity RNA polymerase II CTD heptapeptide repeat kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling biological regulation positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction positive regulation of signaling viral gene expression biological process involved in interspecies interaction between organisms negative regulation by host of viral transcription modulation by host of symbiont process viral process biological process involved in interaction with symbiont viral transcription biological process involved in symbiotic interaction adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of alpha-beta T cell activation regulation of leukocyte activation regulation of cell activation positive regulation of T cell differentiation alpha-beta T cell differentiation involved in immune response regulation of cell development multicellular organism development positive regulation of immune response T cell activation cell differentiation regulation of T-helper cell differentiation alpha-beta T cell activation regulation of immune system process positive regulation of CD4-positive, alpha-beta T cell differentiation immune response T-helper cell differentiation alpha-beta T cell lineage commitment positive regulation of cell development immune effector process regulation of leukocyte cell-cell adhesion T-helper 17 cell differentiation cell fate commitment CD4-positive or CD8-positive, alpha-beta T cell lineage commitment positive regulation of alpha-beta T cell differentiation regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cell development positive regulation of leukocyte cell-cell adhesion CD4-positive, alpha-beta T cell differentiation positive regulation of T-helper 17 cell differentiation positive regulation of T-helper cell differentiation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation alpha-beta T cell differentiation T cell activation involved in immune response positive regulation of cell differentiation leukocyte activation involved in immune response positive regulation of immune effector process regulation of cell-cell adhesion regulation of T-helper 17 cell differentiation hemopoiesis regulation of cell adhesion cell activation positive regulation of T-helper 17 type immune response regulation of CD4-positive, alpha-beta T cell activation immune system process regulation of lymphocyte activation regulation of immune effector process multicellular organismal process regulation of leukocyte differentiation mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation cell activation involved in immune response CD4-positive, alpha-beta T cell differentiation involved in immune response positive regulation of developmental process positive regulation of cell activation positive regulation of T-helper 17 cell lineage commitment anatomical structure development positive regulation of leukocyte activation T cell differentiation positive regulation of adaptive immune response CD4-positive, alpha-beta T cell lineage commitment positive regulation of immune system process developmental process positive regulation of T cell activation regulation of adaptive immune response T-helper cell lineage commitment T-helper 17 cell lineage commitment positive regulation of alpha-beta T cell activation regulation of immune response positive regulation of multicellular organismal process leukocyte differentiation cellular developmental process regulation of CD4-positive, alpha-beta T cell differentiation regulation of alpha-beta T cell differentiation lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of CD4-positive, alpha-beta T cell activation cell adhesion regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains cell-cell adhesion alpha-beta T cell activation involved in immune response positive regulation of hemopoiesis CD4-positive, alpha-beta T cell activation regulation of multicellular organismal process lymphocyte activation involved in immune response positive regulation of cell fate commitment regulation of lymphocyte differentiation regulation of multicellular organismal development regulation of T-helper 17 cell lineage commitment regulation of T-helper 17 type immune response regulation of cell fate commitment positive regulation of cell adhesion regulation of T cell activation T cell differentiation involved in immune response T cell lineage commitment adaptive immune response positive T cell selection regulation of hemopoiesis positive regulation of leukocyte differentiation T cell selection positive regulation of lymphocyte differentiation T-helper 17 type immune response regulation of cell cycle phase transition negative regulation of biological process regulation of cellular response to stress negative regulation of cell cycle regulation of cell cycle checkpoint negative regulation of cell cycle phase transition cell cycle regulation of cell cycle process DNA integrity checkpoint signaling negative regulation of DNA damage checkpoint negative regulation of cell cycle checkpoint DNA damage checkpoint signaling negative regulation of signaling negative regulation of intracellular signal transduction cell cycle phase transition negative regulation of cell communication regulation of response to stress negative regulation of cellular process positive regulation of cell cycle process regulation of cell cycle cell cycle process negative regulation of response to stimulus negative regulation of cell cycle process negative regulation of signal transduction positive regulation of cell cycle cell cycle checkpoint signaling positive regulation of cell cycle phase transition signal transduction in response to DNA damage regulation of DNA damage checkpoint regulation of defense response regulation of response to external stimulus defense response regulation of inflammatory response response to external stimulus inflammatory response positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of cellular biosynthetic process transcription by RNA polymerase II regulation of transcription by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II transcription elongation by RNA polymerase II positive regulation of transcription elongation by RNA polymerase II positive regulation of DNA-templated transcription, elongation DNA-templated transcription elongation G2/M transition of mitotic cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of mitotic cell cycle cell cycle G2/M phase transition positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition regulation of mitotic cell cycle phase transition mitotic cell cycle process mitotic cell cycle phase transition cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen nuclear chromosome chromosome cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle condensed chromosome non-membrane-bounded organelle nuclear lumen nucleoplasm
B [auth D]	NAD-dependent protein deacetylase sirtuin-7	catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity protein-glutaryllysine deglutarylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds protein-malonyllysine demalonylase activity chromatin binding binding transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity deacetylase activity catalytic activity, acting on a protein hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides hydrolase activity protein-glutaryllysine deglutarylase activity catalytic activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds protein-malonyllysine demalonylase activity chromatin binding binding transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity deacetylase activity NAD-dependent histone deacetylase activity NAD-dependent histone H3K18 deacetylase activity protein lysine deacetylase activity histone deacetylase activity histone H3K deacetylase activity histone modifying activity NAD-dependent protein lysine deacetylase activity NAD+ binding NAD binding nucleotide binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding heterocyclic compound binding small molecule binding protein-succinyllysine desuccinylase activity protein-propionyllysine depropionylase activity cation binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process monosaccharide metabolic process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process monosaccharide metabolic process regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process cellular metabolic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process regulation of cellular metabolic process regulation of cellular biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process biosynthetic process regulation of gluconeogenesis metabolic process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process glucose metabolic process developmental process multicellular organismal process cellular developmental process ossification cell differentiation osteoblast differentiation ribonucleoprotein complex biogenesis RNA metabolic process rRNA processing positive regulation of rRNA processing nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process positive regulation of nucleobase-containing compound metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization DNA-templated transcription transcription by RNA polymerase II chromatin organization chromatin remodeling transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling R-loop processing negative regulation of cellular process negative regulation of biological process retrotransposon silencing transposition retrotransposition negative regulation of post-translational protein modification regulation of protein modification process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal DNA repair-dependent chromatin remodeling meiotic chromosome segregation sexual reproduction reproductive process meiotic cell cycle organelle fission chromosome organization meiotic cell cycle process chromosome organization involved in meiotic cell cycle nuclear division organelle organization meiosis I meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation meiotic nuclear division homologous chromosome segregation cell cycle chromosome segregation cell cycle process protein localization regulation of localization establishment of protein localization cellular localization nitrogen compound transport regulation of protein localization nucleocytoplasmic transport transport nuclear transport localization cellular macromolecule localization establishment of localization in cell regulation of protein export from nucleus nuclear export regulation of intracellular transport regulation of transport regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport regulation of protein transport protein export from nucleus establishment of localization protein transport regulation of cellular localization macromolecule localization regulation of intracellular protein transport intracellular protein transport protein deacylation protein deglutarylation macromolecule deacylation negative regulation of cellular metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of cellular component organization regulation of organelle organization regulation of mitochondrion organization mitochondrion organization protein deacetylation DNA metabolic process DNA repair rRNA transcription regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction signaling negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of DNA-templated transcription transcription by RNA polymerase I positive regulation of transcription by RNA polymerase I regulation of RNA biosynthetic process regulation of transcription by RNA polymerase I positive regulation of RNA biosynthetic process regulation of DNA-templated transcription regulation of transcription of nucleolar large rRNA by RNA polymerase I nucleolar large rRNA transcription by RNA polymerase I regulation of transcription by RNA polymerase II negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of RNA metabolic process regulation of cellular response to stress regulation of response to stress regulation of DNA repair regulation of DNA metabolic process protein depropionylation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nuclear speck nuclear body nucleoplasm cytoplasm nucleolar chromatin nuclear chromosome chromosome chromatin nucleolus organizer region site of double-strand break site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR043508	Brdt, bromodomain, repeat I	Domain
A, C [auth B]	IPR027353	NET domain	Domain
A, C [auth B]	IPR043509	Brdt, bromodomain, repeat II	Domain
A, C [auth B]	IPR018359	Bromodomain, conserved site	Conserved Site
A, C [auth B]	IPR001487	Bromodomain	Domain
A, C [auth B]	IPR050935	Bromodomain-containing chromatin reader	Family
A, C [auth B]	IPR038336	NET domain superfamily	Homologous Superfamily
A, C [auth B]	IPR031354	Bromodomain protein 4, C-terminal	Domain
A, C [auth B]	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
B [auth D]	IPR026590	Sirtuin family, catalytic core domain	Domain
B [auth D]	IPR003000	Sirtuin family	Family
B [auth D]	IPR029035	DHS-like NAD/FAD-binding domain superfamily	Homologous Superfamily
B [auth D]	IPR050134	NAD-dependent sirtuin protein deacylases	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: O60885	osteosarcoma medulloblastoma glioblastoma melanotic medulloblastoma adult medulloblastoma thyroid adenoma alopecia prostate cancer Cornelia de Lange syndrome pulmonary hypertension giant cell glioblastoma hyperplasia malignant colon neoplasm medullomyoblastoma with myogenic differentiation autosomal dominant polycystic kidney disease osteosarcoma medulloblastoma glioblastoma melanotic medulloblastoma adult medulloblastoma thyroid adenoma alopecia prostate cancer Cornelia de Lange syndrome pulmonary hypertension giant cell glioblastoma hyperplasia malignant colon neoplasm medullomyoblastoma with myogenic differentiation autosomal dominant polycystic kidney disease childhood medulloblastoma thyroid gland carcinoma juvenile dermatomyositis mature T-cell and NK-cell non-Hodgkin lymphoma ovarian cancer polycystic kidney disease 2 androgenetic alopecia Post-essential thrombocythaemia myelofibrosis benign colon neoplasm primary myelofibrosis colonic neoplasm Cornelia de Lange syndrome 3 hematologic disease lung cancer nut midline carcinoma pancreatic ductal adenocarcinoma astrocytic tumor cancer desmoplastic/nodular medulloblastoma thyroid cancer tuberculosis plasma cell myeloma primary cutaneous T-cell lymphoma Cornelia de Lange syndrome 2 rheumatoid arthritis drug-induced liver injury
B [auth D]	Pharos: Q9NRC8	attention deficit hyperactivity disorder, inattentive type ischemia reperfusion injury pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Steatohepatitis pancreatic intraductal papillary-mucinous carcinoma psoriasis fatty liver disease pancreatic intraductal papillary-mucinous neoplasm systemic sclerosis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth D]	ALY	Parent Component: LYS RESID: AA0055 PSI-MOD : N6-acetyl-L-lysine MOD:00064

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.