5NNE | pdb_00005nne

Crystal Structure of the first bromodomain of human BRD4 in complex with a diacetylated TOP2A peptide (K1201ac/K1204ac)

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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	VP4_haemagglut	e5nneA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: VP4_haemagglut	ECOD (v294.1)

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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B [auth C]	GKA(ALY)GK(ALY)TQMY	ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding ATP-dependent activity, acting on DNA catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity ATP-dependent activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding chromatin binding protein heterodimerization activity protein binding protein dimerization activity ubiquitin binding ubiquitin-like protein binding RNA binding cation binding magnesium ion binding metal ion binding identical protein binding protein homodimerization activity kinase binding protein kinase C binding enzyme binding protein kinase binding DNA binding, bending nucleic acid conformation isomerase activity isomerase activity DNA topoisomerase activity DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity macromolecular conformation isomerase activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development regulation of single stranded viral RNA replication via double stranded DNA intermediate cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process developmental process multicellular organism development multicellular organismal process embryonic cleavage anatomical structure development cell division embryo development regulation of single stranded viral RNA replication via double stranded DNA intermediate regulation of cellular process positive regulation of biological process RNA metabolic process viral life cycle 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 regulation of RNA metabolic process positive regulation of single stranded viral RNA replication via double stranded DNA intermediate positive regulation of biosynthetic process viral RNA genome replication viral process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process positive regulation of viral genome replication positive regulation of viral process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process single stranded viral RNA replication via double stranded DNA intermediate nucleic acid metabolic process positive regulation of RNA metabolic process regulation of viral life cycle regulation of viral process biosynthetic process viral genome replication positive regulation of RNA biosynthetic process regulation of viral genome replication metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process cell cycle chromosome segregation cell cycle process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death chromosome organization DNA conformation change DNA metabolic process cellular component organization DNA topological change organelle organization cellular component organization or biogenesis positive regulation of DNA-templated transcription DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II gene expression regulation of gene expression regulation of DNA-templated transcription chromatin organization rhythmic process circadian rhythm regulation of circadian rhythm sexual reproduction homologous recombination reproductive process resolution of meiotic recombination intermediates meiotic cell cycle process meiosis I meiotic nuclear division reciprocal homologous recombination meiotic cell cycle DNA recombination organelle fission reciprocal meiotic recombination nuclear division meiosis I cell cycle process multicellular organismal reproductive process female gamete generation gamete generation female meiotic nuclear division cellular component disassembly execution phase of apoptosis apoptotic chromosome condensation chromosome condensation cellular component disassembly involved in execution phase of apoptosis apoptotic nuclear changes nuclear chromosome segregation sister chromatid segregation cellular developmental process hemopoiesis cell differentiation cell development hematopoietic progenitor cell differentiation	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle male germ cell nucleus nucleus germ cell nucleus intracellular membrane-bounded organelle DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex membrane-enclosed lumen cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle male germ cell nucleus nucleus germ cell nucleus intracellular membrane-bounded organelle DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex protein-containing complex catalytic complex membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen chromosome condensed chromosome chromosome, centromeric region chromosomal region nucleoplasm ribonucleoprotein complex
A	Bromodomain-containing protein 4	p53 binding protein binding binding RNA polymerase binding RNA polymerase II complex binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding histone H4K12ac reader activity histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity p53 binding protein binding binding RNA polymerase binding RNA polymerase II complex binding RNA polymerase II C-terminal domain binding RNA polymerase core enzyme binding enzyme binding histone H4K12ac reader activity histone reader activity histone H4 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding histone H4K5ac reader activity histone H4K8ac reader activity transcription regulator activity transcription coregulator activity chromatin binding histone H3 reader activity histone H3K27ac reader activity transcription coactivator activity histone H4K16ac reader activity histone H3K9ac reader activity protein serine/threonine kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein-containing complex binding P-TEFb complex binding RNA polymerase II CTD heptapeptide repeat modifying activity RNA polymerase II CTD heptapeptide repeat kinase activity	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 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 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 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 RNA 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic 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 biological process involved in interspecies interaction between organisms host-mediated suppression of viral proces host-mediated perturbation of viral transcription host-mediated suppression of viral transcription host-mediated perturbation of viral process modulation of process of another organism host-mediated perturbation of symbiont process transcription by RNA polymerase II 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 regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II positive regulation of transcription by RNA polymerase II 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 intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen nucleoplasm chromatin

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C]	IPR013506	DNA topoisomerase, type IIA, subunit B, domain 2	Domain
B [auth C]	IPR006171	TOPRIM domain	Domain
B [auth C]	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
B [auth C]	IPR034157	DNA topoisomerase 2, TOPRIM domain	Domain
B [auth C]	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
B [auth C]	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily
B [auth C]	IPR031660	C-terminal associated domain of TOPRIM	Domain
B [auth C]	IPR002205	DNA topoisomerase, type IIA, domain A	Domain
B [auth C]	IPR001154	DNA topoisomerase II, eukaryotic-type	Family
B [auth C]	IPR018522	DNA topoisomerase, type IIA, conserved site	Conserved Site
B [auth C]	IPR013760	DNA topoisomerase, type IIA-like domain superfamily	Homologous Superfamily
B [auth C]	IPR013758	DNA topoisomerase, type IIA, domain A, alpha-beta	Homologous Superfamily
B [auth C]	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
B [auth C]	IPR001241	DNA topoisomerase, type IIA	Family
B [auth C]	IPR012542	DTHCT	Domain
B [auth C]	IPR013757	DNA topoisomerase, type IIA, alpha-helical domain superfamily	Homologous Superfamily
B [auth C]	IPR013759	DNA topoisomerase, type IIA, subunit B, C-terminal	Homologous Superfamily
B [auth C]	IPR050634	DNA Topoisomerase II	Family
A	IPR043508	Brdt, bromodomain, repeat I	Domain
A	IPR027353	NET domain	Domain
A	IPR043509	Brdt, bromodomain, repeat II	Domain
A	IPR018359	Bromodomain, conserved site	Conserved Site
A	IPR001487	Bromodomain	Domain
A	IPR050935	Bromodomain-containing chromatin reader	Family
A	IPR038336	NET domain superfamily	Homologous Superfamily
A	IPR031354	Bromodomain protein 4, C-terminal	Domain
A	IPR036427	Bromodomain-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth C]	Pharos: P11388	adrenal cortex carcinoma breast carcinoma malignant glioma polycystic ovary syndrome neuroblastoma ovarian cancer prostate cancer leukemia lung adenocarcinoma breast cancer mixed glioma adenoid cystic carcinoma salivary gland adenoid cystic carcinoma small cell lung carcinoma Disease Exacerbation adrenal cortex carcinoma breast carcinoma malignant glioma polycystic ovary syndrome neuroblastoma ovarian cancer prostate cancer leukemia lung adenocarcinoma breast cancer mixed glioma adenoid cystic carcinoma salivary gland adenoid cystic carcinoma small cell lung carcinoma Disease Exacerbation thyroid cancer ductal breast carcinoma in situ urinary bladder cancer esophageal adenocarcinoma nasopharyngeal carcinoma glioma acute lymphoblastic leukemia Hodgkins lymphoma pancreatic intraductal papillary-mucinous neoplasm acute promyelocytic leukemia plasma cell myeloma adrenal carcinoma atopic eczema bone osteosarcoma malignant colon neoplasm salivary gland cancer Burkitt lymphoma sinusitis cystic fibrosis medulloblastoma endometriosis hepatocellular carcinoma non-small cell lung carcinoma acute monocytic leukemia IgA glomerulonephritis pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia invasive ductal breast carcinoma kidney Wilms tumor atypical teratoid rhabdoid tumor relapsing-remitting multiple sclerosis malignant ependymoma cancer Sjogren syndrome testicular cancer ulcerative colitis glioblastoma oligodendroglioma acute myeloid leukemia interstitial cystitis pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma Kaposi's sarcoma primitive neuroectodermal tumor astrocytic tumor large cell medulloblastoma psoriasis lung cancer malignant pancreatic neoplasm
A	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 thyroid cancer desmoplastic/nodular medulloblastoma tuberculosis plasma cell myeloma primary cutaneous T-cell lymphoma Cornelia de Lange syndrome 2 rheumatoid arthritis drug-induced liver injury