4YAB | pdb_00004yab

Crystal structure of TRIM24 PHD-bromodomain complexed with 1-methyl-5-(2-methyl-1 3-thiazol-4-yl)-2 3-dihydro-1H-indol-2-one (1)

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Bromodomain	8084277	3001843	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bromodomain	8084277	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		e4yabA1	A: Carbon-nitrogen hydrolase-like	X: Metallo-dependent phosphatases	H: Metallo-dependent phosphatases	T: GCD14	F:	ECOD (20:10:01)
B		e4yabB1	A: Carbon-nitrogen hydrolase-like	X: Metallo-dependent phosphatases	H: Metallo-dependent phosphatases	T: GCD14	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
A	1.20.920.10	Mainly Alpha	Up-down Bundle	Histone Acetyltransferase	Chain A	CATH (4.3.0)
B	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
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, 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
A, B	PF00628	PHD-finger (PHD)	PHD-finger	PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains [2]. Several PHD fingers have been identified as binding modules of methylated histone H3 [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Transcription intermediary factor 1-alpha	p53 binding protein binding binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3K23ac reader activity molecular adaptor activity signaling receptor binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity p53 binding protein binding binding histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity histone H3K23ac reader activity molecular adaptor activity signaling receptor binding chromatin binding transcription coactivator activity transcription regulator activity transcription coregulator activity aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity ubiquitin-like protein ligase activity ubiquitin protein ligase activity transferase activity catalytic activity ubiquitin-protein transferase activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding estrogen response element binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding kinase activity protein kinase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process response to stimulus response to hormone response to chemical response to endogenous stimulus response to peptide hormone response to oxygen-containing compound response to nitrogen compound regulation of vitamin D receptor signaling pathway cellular response to stimulus response to nutrient levels regulation of response to nutrient levels intracellular receptor signaling pathway response to lipid signaling regulation of signal transduction response to vitamin hormone-mediated signaling pathway intracellular signal transduction cell communication cellular response to vitamin D cellular response to endogenous stimulus response to vitamin D regulation of intracellular signal transduction signal transduction cellular response to hormone stimulus regulation of signaling response to nutrient cellular response to oxygen-containing compound vitamin D receptor signaling pathway cellular response to nutrient levels cellular response to chemical stimulus cellular response to vitamin regulation of response to stimulus cellular response to lipid regulation of cell communication cellular response to nutrient nuclear receptor-mediated signaling pathway positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process transcription by RNA polymerase II catabolic process protein catabolic process protein metabolic process macromolecule catabolic process regulation of apoptotic process apoptotic process regulation of programmed cell death cell death programmed cell death protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal regulation of protein stability regulation of biological quality inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis cell population proliferation epithelial cell proliferation response to estrogen cellular response to estrogen stimulus signal transduction by p53 class mediator regulation of signal transduction by p53 class mediator negative regulation of cell population proliferation regulation of cell population proliferation regulation of epithelial cell proliferation negative regulation of epithelial cell proliferation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen perichromatin fibrils nuclear chromosome intracellular membraneless organelle chromosome membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen perichromatin fibrils nuclear chromosome intracellular membraneless organelle chromosome chromatin intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen cytosol nucleoplasm euchromatin male germ cell nucleus germ cell nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR018359	Bromodomain, conserved site	Conserved Site
A, B	IPR001487	Bromodomain	Domain
A, B	IPR019787	Zinc finger, PHD-finger	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A, B	IPR017907	Zinc finger, RING-type, conserved site	Conserved Site
A, B	IPR000315	B-box-type zinc finger	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR036427	Bromodomain-like superfamily	Homologous Superfamily
A, B	IPR003649	B-box, C-terminal	Domain
A, B	IPR001841	Zinc finger, RING-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O15164	Liver Cirrhosis, Experimental atypical teratoid rhabdoid tumor glioblastoma medulloblastoma ovarian serous adenocarcinoma thyroid gland papillary carcinoma cancer hepatocellular carcinoma lung cancer oligodendroglioma pilocytic astrocytoma cystic fibrosis malignant glioma osteosarcoma primitive neuroectodermal tumor Liver Cirrhosis, Experimental atypical teratoid rhabdoid tumor glioblastoma medulloblastoma ovarian serous adenocarcinoma thyroid gland papillary carcinoma cancer hepatocellular carcinoma lung cancer oligodendroglioma pilocytic astrocytoma cystic fibrosis malignant glioma osteosarcoma primitive neuroectodermal tumor squamous cell lung carcinoma

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.