5FB0

Crystal Structure of a PHD finger bound to histone H3 T3ph peptide

External Resource: Annotation

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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00439	e5fb0A1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: PF00439	ECOD (1.6)
A	PF00628	e5fb0A2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF00628	ECOD (1.6)
C	PF00439	e5fb0C1	A: alpha bundles	X: Bromodomain-like	H: Bromodomain (From Topology)	T: Bromodomain	F: PF00439	ECOD (1.6)
C	PF00628	e5fb0C2	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PF00628	ECOD (1.6)

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)
C	3.30.40.10	Alpha Beta	2-Layer Sandwich	Herpes Virus-1	Zinc/RING finger domain, C3HC4 (zinc finger)	CATH (4.3.0)
C	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
B [auth D], D [auth F]	PF00125	Core histone H2A/H2B/H3/H4 (Histone)	Core histone H2A/H2B/H3/H4	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D], D [auth F]	Peptide from Histone H3	DNA binding binding organic cyclic compound binding nucleic acid binding cell adhesion molecule binding cadherin binding protein binding protein heterodimerization activity protein dimerization activity structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 organic substance metabolic process protein-containing complex organization protein-DNA complex assembly protein-DNA complex organization cellular component 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 organic substance metabolic process biosynthetic process cellular biosynthetic process cellular metabolic process organic substance biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of cellular process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression 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 metabolic process	membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex membrane cellular anatomical entity extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome chromatin chromosome intracellular organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, C	Nuclear autoantigen Sp-100	protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromo shadow domain binding DNA binding organic cyclic compound binding nucleic acid binding kinase binding enzyme binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity protein binding binding protein domain specific binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding chromo shadow domain binding DNA binding organic cyclic compound binding nucleic acid binding kinase binding enzyme binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity identical protein binding protein homodimerization activity protein dimerization activity	regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process cellular process developmental process multicellular organismal process regulation of multicellular organismal development regulation of developmental process blood vessel morphogenesis tube development angiogenesis vasculature development regulation of vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis regulation of angiogenesis anatomical structure development anatomical structure formation involved in morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development negative regulation of DNA-binding transcription factor activity negative regulation of molecular function regulation of molecular function regulation of DNA-binding transcription factor activity cellular response to stimulus regulation of signaling response to stimulus cell surface receptor signaling pathway signaling regulation of signal transduction cell communication Fas signaling pathway regulation of response to stimulus regulation of cell communication signal transduction regulation of Fas signaling pathway protein localization negative regulation of protein transport regulation of localization establishment of protein localization negative regulation of nucleocytoplasmic transport nitrogen compound transport nucleocytoplasmic transport nuclear transport negative regulation of intracellular protein transport negative regulation of transport localization establishment of localization in cell cellular macromolecule localization nuclear export regulation of protein export from nucleus regulation of intracellular transport organic substance transport negative regulation of establishment of protein localization intracellular transport regulation of nucleocytoplasmic transport protein localization to nucleus protein export from nucleus establishment of localization maintenance of location regulation of intracellular protein transport intracellular protein transport maintenance of protein location cellular localization regulation of protein localization transport maintenance of location in cell maintenance of protein location in cell negative regulation of protein export from nucleus negative regulation of protein localization negative regulation of intracellular transport regulation of transport regulation of establishment of protein localization maintenance of protein location in nucleus regulation of protein transport protein transport regulation of cellular localization macromolecule localization protein localization to organelle maintenance of protein localization in organelle positive regulation of DNA-binding transcription factor activity positive regulation of molecular function extrinsic apoptotic signaling pathway via death domain receptors regulation of programmed cell death extrinsic apoptotic signaling pathway regulation of apoptotic process cell death regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway regulation of extrinsic apoptotic signaling pathway via death domain receptors apoptotic process programmed cell death regulation of apoptotic signaling pathway intracellular receptor signaling pathway retinoic acid receptor signaling pathway response to retinoic acid response to organic substance response to lipid response to chemical response to oxygen-containing compound response to cytokine telomere organization chromosome organization DNA metabolic process telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis biological process involved in interspecies interaction between organisms immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus response to type I interferon response to type II interferon cytokine-mediated signaling pathway cellular response to type II interferon interferon-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance type II interferon-mediated signaling pathway cellular response to chemical stimulus negative regulation of locomotion regulation of cell motility endothelial cell migration negative regulation of endothelial cell migration tissue migration negative regulation of epithelial cell migration ameboidal-type cell migration regulation of cell migration regulation of endothelial cell migration cell migration epithelial cell migration cell motility regulation of epithelial cell migration locomotion negative regulation of cell migration epithelium migration regulation of locomotion negative regulation of cell motility negative regulation of multicellular organismal process viral gene expression regulation of viral process negative regulation of viral process regulation of viral transcription negative regulation of viral transcription viral process viral transcription regulation of DNA binding regulation of binding negative regulation of binding negative regulation of DNA binding signal transduction by p53 class mediator DNA damage response, signal transduction by p53 class mediator intracellular signal transduction cellular response to stress DNA damage response signal transduction in response to DNA damage transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process cellular response to type I interferon type I interferon-mediated signaling pathway	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity nucleolus intracellular organelle lumen intracellular organelle organelle lumen organelle intracellular non-membrane-bounded organelle nuclear lumen non-membrane-bounded organelle nuclear periphery cytoplasm nucleoplasm nuclear body chromosome chromosome, telomeric region chromosomal region PML body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], D [auth F]	IPR009072	Histone-fold	Homologous Superfamily
B [auth D], D [auth F]	IPR007125	Histone H2A/H2B/H3	Domain
B [auth D], D [auth F]	IPR000164	Histone H3/CENP-A	Family
A, C	IPR000770	SAND domain	Domain
A, C	IPR004865	HSR domain	Domain
A, C	IPR043563	Nuclear body protein Sp110/Sp140/Sp140L-like	Family
A, C	IPR010919	SAND-like domain superfamily	Homologous Superfamily
A, C	IPR009071	High mobility group box domain	Domain
A, C	IPR036910	High mobility group box domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth D], D [auth F]	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma allergic rhinitis ovarian cancer autism spectrum disorder psoriasis cutaneous lupus erythematosus tuberculosis ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis astrocytoma (excluding glioblastoma) pancreatic intraductal papillary-mucinous carcinoma breast cancer spina bifida cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm breast carcinoma subependymoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma
A, C	Pharos: P23497	breast cancer glioblastoma lung carcinoma non-small cell lung carcinoma pilocytic astrocytoma psoriasis ulcerative colitis cutaneous lupus erythematosus juvenile dermatomyositis malignant ependymoma osteosarcoma pituitary cancer rheumatoid arthritis dermatomyositis lung cancer breast cancer glioblastoma lung carcinoma non-small cell lung carcinoma pilocytic astrocytoma psoriasis ulcerative colitis cutaneous lupus erythematosus juvenile dermatomyositis malignant ependymoma osteosarcoma pituitary cancer rheumatoid arthritis dermatomyositis lung cancer malignant glioma ovarian cancer plasma cell myeloma subependymal giant cell astrocytoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth D], D [auth F]	TPO	Parent Component: THR RESID: AA0038 PSI-MOD : O-phospho-L-threonine MOD:00047

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.