2L75

Solution structure of CHD4-PHD2 in complex with H3K9me3

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	FYVE/PHD zinc finger	8032792	3001459	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	PHD_1	e2l75A1	A: few secondary structure elements	X: RING/U-box-like	H: RING/U-box-like	T: FYVE/PHD zinc finger	F: PHD_1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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
B	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
A	Chromodomain-helicase-DNA-binding protein 4	protein binding binding histone binding histone deacetylase binding enzyme binding transcription factor binding transcription coregulator binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding protein binding binding histone binding histone deacetylase binding enzyme binding transcription factor binding transcription coregulator binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding protein-containing complex binding chromatin binding ATP-dependent activity, acting on DNA ATP-dependent chromatin remodeler activity catalytic activity, acting on DNA transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides cation binding transition metal ion binding zinc ion binding metal ion binding	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process multicellular organismal process regulation of cellular component organization cellular component organization developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation cellular process multicellular organismal process regulation of cellular component organization cellular component organization cellular component biogenesis multicellular organism development cellular component assembly cell junction assembly anatomical structure development regulation of synapse structure or activity regulation of synapse assembly synapse organization cellular component organization or biogenesis regulation of biological quality system development nervous system development regulation of cellular component biogenesis regulation of cell junction assembly regulation of synapse organization cell junction organization synapse assembly 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 transcription by RNA polymerase II organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II 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 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 presynapse organization terminal button organization regulation of cell fate commitment cell fate specification regulation of cell fate specification cell fate commitment cellular response to stimulus double-strand break repair response to stimulus DNA recombination DNA metabolic process cellular response to stress DNA damage response response to stress recombinational repair double-strand break repair via homologous recombination DNA repair 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 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 negative regulation of gene expression protein-DNA complex organization protein-containing complex organization chromatin organization chromatin remodeling	membrane cellular anatomical entity neuron to neuron synapse synapse cell junction asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse intracellular anatomical structure cytoplasm intracellular organelle protein-containing complex membrane cellular anatomical entity neuron to neuron synapse synapse cell junction asymmetric synapse cerebellar granule cell to Purkinje cell synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse intracellular anatomical structure cytoplasm intracellular organelle protein-containing complex protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle membrane-bounded organelle ATPase complex nucleus membrane-enclosed lumen nuclear protein-containing complex transcription regulator complex intracellular organelle lumen histone deacetylase complex nucleoplasm NuRD complex SWI/SNF superfamily-type complex catalytic complex intracellular membrane-bounded organelle organelle lumen CHD-type complex nuclear lumen chromosome, telomeric region chromosomal region RNA polymerase II transcription regulator complex centrosome microtubule organizing center cytoskeleton microtubule cytoskeleton site of DNA damage
B	14-meric peptide from 1Histone H3.1	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001965	Zinc finger, PHD-type	Domain
A	IPR049730	SNF2/RAD5-like, C-terminal helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR012958	CHD, N-terminal	Domain
A	IPR012957	CHD, C-terminal 2	Domain
A	IPR000330	SNF2, N-terminal	Domain
A	IPR023780	Chromo domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR019787	Zinc finger, PHD-finger	Domain
A	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A	IPR002464	DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site	Conserved Site
A	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site
A	IPR038718	SNF2-like, N-terminal domain superfamily	Homologous Superfamily
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR009462	CHD subfamily II, SANT-like domain	Domain
A	IPR009463	Domain of unknown function DUF1087	Domain
B	IPR009072	Histone-fold	Homologous Superfamily
B	IPR007125	Histone H2A/H2B/H3	Domain
B	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q14839	Sifrim-Hitz-Weiss syndrome endometrial carcinoma intellectual disability schizophrenia astrocytic tumor endometrial cancer glioblastoma lung adenocarcinoma osteosarcoma psoriasis autism malignant mesothelioma ovarian cancer rheumatoid arthritis developmental disability Sifrim-Hitz-Weiss syndrome endometrial carcinoma intellectual disability schizophrenia astrocytic tumor endometrial cancer glioblastoma lung adenocarcinoma osteosarcoma psoriasis autism malignant mesothelioma ovarian cancer rheumatoid arthritis developmental disability Endometrial Neoplasms large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor
B	Pharos: P68431	lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial lung carcinoma glioblastoma glioma large cell medulloblastoma malignant mesothelioma non-small cell lung carcinoma ovarian cancer allergic rhinitis psoriasis autism spectrum disorder tuberculosis cutaneous lupus erythematosus ependymoma gastric carcinoma Glioma of Brain, Familial hypertensive disorder lung adenocarcinoma malignant colon neoplasm malignant pancreatic neoplasm osteoarthritis pancreatic intraductal papillary-mucinous carcinoma astrocytoma (excluding glioblastoma) spina bifida breast cancer cystic fibrosis exocrine pancreatic carcinoma glioma susceptibility 1 invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm atypical teratoid rhabdoid tumor subependymoma breast carcinoma ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma