5E7D | pdb_00005e7d

Crystal Structure of the fifth bromodomain of human PB1 in complex with a hydroxyphenyl ligand

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d5e7dd_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5e7dc_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5e7db_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5e7da_	All alpha proteins	Bromodomain-like	Bromodomain	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D		e5e7dD1	A: ALDH-like	X: ALDH-like	H: ALDH-like	T: PRP38	F:	ECOD (20:10:01)
C		e5e7dC1	A: ALDH-like	X: ALDH-like	H: ALDH-like	T: PRP38	F:	ECOD (20:10:01)
B		e5e7dB1	A: ALDH-like	X: ALDH-like	H: ALDH-like	T: PRP38	F:	ECOD (20:10:01)
A		e5e7dA1	A: ALDH-like	X: ALDH-like	H: ALDH-like	T: PRP38	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
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, 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
A, B, C, D	Protein polybromo-1	chromatin binding binding DNA binding nucleic acid binding	cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress cellular response to stimulus regulation of cellular process response to stimulus regulation of double-strand break repair positive regulation of biological process regulation of cellular response to stress regulation of primary metabolic process positive regulation of response to stimulus nucleobase-containing compound metabolic process positive regulation of metabolic process positive regulation of DNA repair cellular response to stress response to stress regulation of response to stress positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process DNA repair double-strand break repair regulation of biological process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process positive regulation of double-strand break repair nucleic acid metabolic process regulation of DNA repair positive regulation of DNA metabolic process regulation of response to stimulus DNA damage response metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of DNA metabolic process cell cycle mitotic cell cycle regulation of chromosome segregation regulation of cell cycle phase transition regulation of metaphase/anaphase transition of cell cycle regulation of cellular component organization cell cycle phase transition regulation of mitotic metaphase/anaphase transition cellular component organization regulation of mitotic cell cycle cellular component organization or biogenesis regulation of cell cycle chromosome segregation cell cycle process regulation of cell cycle process chromosome organization sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition organelle organization mitotic cell cycle process regulation of sister chromatid segregation nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition developmental process regulation of developmental process cellular developmental process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation myoblast differentiation nucleotide-excision repair regulation of nucleotide-excision repair negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process regulation of G0 to G1 transition G0 to G1 transition transcription elongation by RNA polymerase II RNA metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process DNA-templated transcription elongation transcription by RNA polymerase II biosynthetic process regulation of RNA metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle multicellular organismal process regulation of leukocyte differentiation regulation of leukocyte activation regulation of cell activation mononuclear cell differentiation lymphocyte differentiation positive regulation of T cell differentiation regulation of cell development multicellular organism development positive regulation of cell activation T cell activation positive regulation of leukocyte activation T cell differentiation regulation of immune system process positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process leukocyte differentiation cell development positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion regulation of T cell differentiation positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of hemopoiesis regulation of multicellular organismal process regulation of cell-cell adhesion regulation of lymphocyte differentiation regulation of multicellular organismal development hemopoiesis positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation immune system process regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation regulation of lymphocyte activation chromatin organization chromatin remodeling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix RSC-type complex ATPase complex membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix RSC-type complex ATPase complex protein-containing complex catalytic complex nuclear protein-containing complex intracellular membraneless organelle chromatin chromosome membraneless organelle SWI/SNF superfamily-type complex SWI/SNF complex nucleoplasm chromosomal region kinetochore chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome nuclear chromosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR037968	Protein polybromo-1, Bromodomain 5	Domain
A, B, C, D	IPR018359	Bromodomain, conserved site	Conserved Site
A, B, C, D	IPR001487	Bromodomain	Domain
A, B, C, D	IPR001025	Bromo adjacent homology (BAH) domain	Domain
A, B, C, D	IPR043151	Bromo adjacent homology (BAH) domain superfamily	Homologous Superfamily
A, B, C, D	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B, C, D	IPR037382	Remodelling complex subunit Rsc/polybromo	Family
A, B, C, D	IPR009071	High mobility group box domain	Domain
A, B, C, D	IPR036910	High mobility group box domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q86U86	renal cell carcinoma cholangiocarcinoma thymoma bipolar disorder intrahepatic cholangiocarcinoma thymic carcinoma papillary renal cell carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma collecting duct carcinoma malignant ependymoma medulloblastoma osteoarthritis pancreatic intraductal papillary-mucinous carcinoma adenoma renal cell carcinoma cholangiocarcinoma thymoma bipolar disorder intrahepatic cholangiocarcinoma thymic carcinoma papillary renal cell carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma collecting duct carcinoma malignant ependymoma medulloblastoma osteoarthritis pancreatic intraductal papillary-mucinous carcinoma adenoma primitive neuroectodermal tumor cancer schizophrenia clear cell papillary renal cell carcinoma Conventional (Clear Cell) Renal Cell Carcinoma glioblastoma malignant glioma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor breast adenocarcinoma rheumatoid arthritis clear cell renal carcinoma endogenous depression Hodgkins lymphoma large cell medulloblastoma ovarian cancer bile duct cancer renal carcinoma breast carcinoma intellectual disability

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.