6V41 | pdb_00006v41

crystal structure of CDY1 chromodomain bound to H3K9me3

External Resource: Annotation

Domain Annotation: ECOD Classification
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 [auth AAA]	Chromo	e6v41AAA1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth AAA]	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
A [auth AAA]	Testis-specific chromodomain protein Y 1	transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K27me3 reader activity protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K27me3 reader activity protein-lysine-acetyltransferase activity catalytic activity, acting on a protein protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity transferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity histone modifying activity acyltransferase activity, transferring groups other than amino-acyl groups catalytic activity N-acyltransferase activity	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B [auth QQQ]	Histone H3.1 Peptide	DNA binding 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 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 biosynthetic process 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 biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process organelle organization telomere organization chromosome organization regulation of biosynthetic process regulation of biological process regulation of cellular process epigenetic regulation of gene expression biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process	cellular anatomical structure membrane 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 cellular anatomical structure membrane 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 intracellular membraneless organelle chromatin chromosome intracellular organelle membraneless 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 [auth AAA]	IPR051053	Enoyl-CoA hydratase/isomerase and chromodomain-containing protein	Family
A [auth AAA]	IPR001753	Enoyl-CoA hydratase/isomerase	Family
A [auth AAA]	IPR000953	Chromo/chromo shadow domain	Domain
A [auth AAA]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A [auth AAA]	IPR023780	Chromo domain	Domain
A [auth AAA]	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A [auth AAA]	IPR014748	Enoyl-CoA hydratase, C-terminal	Homologous Superfamily
A [auth AAA]	IPR023779	Chromo domain, conserved site	Conserved Site
A [auth AAA]	IPR017984	Chromo domain subgroup	Domain
B [auth QQQ]	IPR009072	Histone-fold	Homologous Superfamily
B [auth QQQ]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B [auth QQQ]	IPR000164	Histone H3/CENP-A	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth AAA]	Pharos: Q9Y6F8	Spermatogenic Failure, Nonobstructive, Y-Linked spermatogenic failure, Y-linked, 2
B [auth QQQ]	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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth QQQ]	M3L	Parent Component: LYS RESID: AA0074 PSI-MOD : N6,N6,N6-trimethyl-L-lysine MOD:00083

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.