7BBP | pdb_00007bbp

Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
D [auth DDD]	SCOP2B Superfamily	Bromodomain	8084279	3001843	SCOP2B (2022-06-29)
C [auth CCC]	SCOP2B Superfamily	Bromodomain	8084279	3001843	SCOP2B (2022-06-29)
B [auth BBB]	SCOP2B Superfamily	Bromodomain	8084279	3001843	SCOP2B (2022-06-29)
A [auth AAA]	SCOP2B Superfamily	Bromodomain	8084279	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)
D [auth DDD]	Radical_SAM	e7bbpDDD1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Radical_SAM	ECOD (v294.1)
C [auth CCC]	Radical_SAM	e7bbpCCC1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Radical_SAM	ECOD (v294.1)
B [auth BBB]	Radical_SAM	e7bbpBBB1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Radical_SAM	ECOD (v294.1)
A [auth AAA]	Radical_SAM	e7bbpAAA1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: Bromodomain	T: Bromodomain	F: Radical_SAM	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	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 FFF], F [auth GGG]	Histone H4	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	PH-interacting protein	protein binding binding signaling receptor binding insulin receptor binding histone reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death developmental process regulation of biological process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process biological regulation negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process cellular process apoptotic process programmed cell death developmental process anatomical structure morphogenesis regulation of developmental process anatomical structure development cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis positive regulation of organelle organization regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process regulation of mitotic nuclear division positive regulation of mitotic nuclear division mitotic cell cycle cellular component organization regulation of mitotic cell cycle positive regulation of cell cycle process cellular component organization or biogenesis cell cycle regulation of cell cycle positive regulation of cellular process cell cycle process mitotic nuclear division regulation of cell cycle process organelle fission positive regulation of nuclear division regulation of organelle organization positive regulation of cell cycle organelle organization nuclear division mitotic cell cycle process regulation of nuclear division regulation of cell shape regulation of biological quality cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation cytoskeleton organization cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling regulation of signal transduction cell surface receptor protein tyrosine kinase signaling pathway cell communication positive regulation of response to stimulus positive regulation of insulin-like growth factor receptor signaling pathway regulation of insulin-like growth factor receptor signaling pathway signal transduction enzyme-linked receptor protein signaling pathway regulation of signaling cell surface receptor signaling pathway insulin-like growth factor receptor signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway cellular response to endogenous stimulus response to hormone cellular response to hormone stimulus response to endogenous stimulus response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to insulin cellular response to insulin stimulus 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 protein phosphorylation regulation of protein modification process regulation of protein phosphorylation phosphorylation regulation of protein metabolic process macromolecule modification phosphate-containing compound metabolic process regulation of phosphorylation regulation of phosphorus metabolic process protein metabolic process protein modification process phosphorus metabolic process negative regulation of signaling extrinsic apoptotic signaling pathway negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of apoptotic signaling pathway transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth FFF], F [auth GGG]	IPR009072	Histone-fold	Homologous Superfamily
E [auth FFF], F [auth GGG]	IPR001951	Histone H4	Family
E [auth FFF], F [auth GGG]	IPR035425	CENP-T/Histone H4, histone fold	Domain
E [auth FFF], F [auth GGG]	IPR019809	Histone H4, conserved site	Conserved Site
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR057451	BRWD/PHIP, ancillary-like domain	Domain
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR019775	WD40 repeat, conserved site	Conserved Site
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR018359	Bromodomain, conserved site	Conserved Site
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR001487	Bromodomain	Domain
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR052060	Bromodomain and WD repeat-containing	Family
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR001680	WD40 repeat	Repeat
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	IPR057452	BRWD/PHIP, N-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth AAA], B [auth BBB], C [auth CCC], D [auth DDD]	Pharos: Q8WWQ0	intellectual disability adrenal cortex carcinoma ductal breast carcinoma in situ Mental deficiency ovarian cancer psoriasis Sjogren syndrome colorectal cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia rheumatoid arthritis developmental delay, intellectual disability, obesity, and dysmorphic features medulloblastoma osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth FFF], F [auth GGG]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.