5JJZ | pdb_00005jjz

Chromo domain of human Chromodomain Protein, Y-Like 2

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	Chromo domain-like	8062263	3000161	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	AhpC-TSA	e5jjzA1	A: a/b three-layered sandwiches	X: Chlorophyll a-b binding protein	H: Chlorophyll a-b binding protein	T: Chlorophyll a-b binding protein	F: AhpC-TSA	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00385	Chromo (CHRromatin Organisation MOdifier) domain (Chromo)	Chromo (CHRromatin Organisation MOdifier) domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	LYS-LYS-LYS-ALA-ARG-MLY-SER-ALA-GLY-ALA-ALA-LYS-TYR	DNA binding double-stranded DNA binding binding nucleic acid binding chromatin binding chromatin DNA binding histone deacetylase binding protein binding enzyme binding protein-containing complex binding nucleosome binding nucleosomal DNA binding RNA binding structural molecule activity DNA binding double-stranded DNA binding binding nucleic acid binding chromatin binding chromatin DNA binding histone deacetylase binding protein binding enzyme binding protein-containing complex binding nucleosome binding nucleosomal DNA binding RNA binding structural molecule activity structural constituent of chromatin	protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 organelle organization protein-containing complex organization protein-DNA complex assembly cellular component organization protein-DNA complex 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 organelle organization chromosome condensation chromosome organization 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 transcription by RNA polymerase II 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 regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription regulation of biological process negative regulation of transcription by RNA polymerase II 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 regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process regulation of DNA recombination DNA recombination DNA metabolic process negative regulation of DNA recombination negative regulation of DNA metabolic process regulation of DNA metabolic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin euchromatin protein-containing complex protein-DNA complex nucleosome membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin euchromatin protein-containing complex protein-DNA complex nucleosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A	Chromodomain Y-like protein 2	transcription corepressor activity transcription regulator activity transcription coregulator activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity histone H3K27me3 reader activity	-	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
B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
B	IPR005818	Linker histone H1/H5, domain H15	Domain
B	IPR005819	Linker histone H1/H5	Family
A	IPR051053	Enoyl-CoA hydratase/isomerase and chromodomain-containing protein	Family
A	IPR000953	Chromo/chromo shadow domain	Domain
A	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A	IPR023780	Chromo domain	Domain
A	IPR001753	Enoyl-CoA hydratase/isomerase-like domain	Domain
A	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A	IPR014748	Enoyl-CoA hydratase, C-terminal	Homologous Superfamily
A	IPR023779	Chromo domain, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P10412	adenoid cystic carcinoma salivary gland adenoid cystic carcinoma squamous cell lung carcinoma breast cancer endogenous depression gout intellectual disability multiple sclerosis allergic rhinitis colorectal cancer gastric cancer hepatocellular carcinoma lung adenocarcinoma osteoarthritis schizophrenia adenoid cystic carcinoma salivary gland adenoid cystic carcinoma squamous cell lung carcinoma breast cancer endogenous depression gout intellectual disability multiple sclerosis allergic rhinitis colorectal cancer gastric cancer hepatocellular carcinoma lung adenocarcinoma osteoarthritis schizophrenia autism spectrum disorder diabetes mellitus gastric carcinoma hypertensive disorder lung cancer Rahman syndrome
A	Pharos: Q8N8U2	subependymal giant cell astrocytoma astrocytic tumor cancer glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pituitary cancer ulcerative colitis atypical teratoid rhabdoid tumor cystic fibrosis inflammatory bowel disease malignant ependymoma nodular sclerosis classical Hodgkin lymphoma ovarian cancer subependymal giant cell astrocytoma astrocytic tumor cancer glioblastoma large cell medulloblastoma medulloblastoma osteosarcoma pituitary cancer ulcerative colitis atypical teratoid rhabdoid tumor cystic fibrosis inflammatory bowel disease malignant ependymoma nodular sclerosis classical Hodgkin lymphoma ovarian cancer primitive neuroectodermal tumor breast carcinoma ductal breast carcinoma in situ invasive ductal breast carcinoma malignant glioma oligodendroglioma pilocytic astrocytoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	MLY	Parent Component: LYS RESID: AA0075 PSI-MOD : N6,N6-dimethyl-L-lysine MOD:00084

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.