2E3K

Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 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
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	8084255	3001843	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bromodomain	8084255	3001843	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bromodomain	8084255	3001843	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bromodomain	8084255	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	e2e3kA1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
B	Bromodomain	e2e3kB1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
C	Bromodomain	e2e3kC1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: Bromodomain	ECOD (1.6)
D	Bromodomain	e2e3kD1	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)
B	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
C	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
E [auth Q], F [auth R]	15-mer peptide from Histone H4	DNA binding binding organic cyclic compound binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin identical protein binding	nucleolar large rRNA transcription by RNA polymerase I cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I nucleolar large rRNA transcription by RNA polymerase I cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process 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 component organization or biogenesis nucleosome assembly nucleosome organization regulation of cellular process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase I positive regulation of cellular process positive regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase I positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle RNA polymerase I upstream activating factor complex RNA polymerase I transcription regulator complex organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle replication fork protection complex nuclear replication fork nuclear chromosome chromosome replication fork protein-DNA complex nucleosome chromatin
A, B, C, D	Bromodomain-containing protein 2	protein binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding 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 binding binding modification-dependent protein binding lysine-acetylated histone binding histone binding acetylation-dependent protein binding 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 chromatin binding	multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process multicellular organismal process embryonic epithelial tube formation chordate embryonic development tube formation embryo development multicellular organism development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching anatomical structure development epithelial tube morphogenesis system development developmental process morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure 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 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains response to stimulus 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 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 response to stimulus 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 positive regulation of cellular process 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 regulation of leukocyte differentiation regulation of cellular process 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 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 regulation of biological 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 positive regulation of biological 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 response to stimulus 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 biological regulation 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 spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation chromatin looping protein localization localization protein localization to chromatin cellular localization protein localization to chromosome protein localization to organelle cellular macromolecule localization macromolecule localization cellular biosynthetic process RNA metabolic process regulation of primary 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic 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 regulation of gene expression biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasm intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth Q], F [auth R]	IPR009072	Histone-fold	Homologous Superfamily
E [auth Q], F [auth R]	IPR035425	CENP-T/Histone H4, histone fold	Domain
E [auth Q], F [auth R]	IPR001951	Histone H4	Family
E [auth Q], F [auth R]	IPR019809	Histone H4, conserved site	Conserved Site
A, B, C, D	IPR043508	Brdt, bromodomain, repeat I	Domain
A, B, C, D	IPR027353	NET domain	Domain
A, B, C, D	IPR043509	Brdt, bromodomain, repeat II	Domain
A, B, C, D	IPR018359	Bromodomain, conserved site	Conserved Site
A, B, C, D	IPR001487	Bromodomain	Domain
A, B, C, D	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B, C, D	IPR050935	Bromodomain-containing chromatin reader	Family
A, B, C, D	IPR038336	NET domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P25440	medulloblastoma childhood medulloblastoma glioblastoma medullomyoblastoma with myogenic differentiation adult medulloblastoma melanotic medulloblastoma dermatomyositis giant cell glioblastoma membranous glomerulonephritis ovarian cancer rheumatoid arthritis ulcerative colitis acute myeloid leukemia astrocytic tumor desmoplastic/nodular medulloblastoma medulloblastoma childhood medulloblastoma glioblastoma medullomyoblastoma with myogenic differentiation adult medulloblastoma melanotic medulloblastoma dermatomyositis giant cell glioblastoma membranous glomerulonephritis ovarian cancer rheumatoid arthritis ulcerative colitis acute myeloid leukemia astrocytic tumor desmoplastic/nodular medulloblastoma intervertebral disc degenerative disorder myopathy pancreatic ductal adenocarcinoma Sjogren syndrome autism spectrum disorder Crohn disease gastric adenocarcinoma hepatitis B virus infection juvenile dermatomyositis osteosarcoma pulmonary hypertension systemic sclerosis allergic rhinitis autoimmune disease inflammatory bowel disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth Q], F [auth R]	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.