5EPL | pdb_00005epl

Crystal Structure of chromodomain of CBX4 in complex with inhibitor UNC3866

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	Chromo domain-like	8062999	3000161	SCOP2B (2022-06-29)
B	SCOP2 Family	Chromo domain	8062998	4000375	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Chromo domain-like	8062999	3000161	SCOP2 (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	Chromo	e5eplA1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
B	Chromo	e5eplB1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)

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)
B	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, B	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, B	E3 SUMO-protein ligase CBX4	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding phosphoprotein binding protein binding chromatin binding RNA binding single-stranded RNA binding aminoacyltransferase activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding phosphoprotein binding protein binding chromatin binding RNA binding single-stranded RNA binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity SUMO transferase activity transferase activity catalytic activity SUMO ligase activity ubiquitin-like protein ligase activity transcription corepressor activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity SUMO binding ubiquitin-like protein binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding enzyme 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 negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death peptidyl-lysine modification protein sumoylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II cellular component organization chromatin organization cellular component organization or biogenesis	membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body membrane-bounded organelle intracellular organelle protein-containing complex cellular anatomical structure intracellular anatomical structure organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle PcG protein complex membrane-enclosed lumen intracellular organelle lumen nuclear speck nuclear body nucleoplasm organelle lumen nuclear lumen PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex
C, D	unc3866	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR023780	Chromo domain	Domain
A, B	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B	IPR033773	CBX family C-terminal motif	Conserved Site
A, B	IPR023779	Chromo domain, conserved site	Conserved Site
A, B	IPR000953	Chromo/chromo shadow domain	Domain
A, B	IPR043531	E3 SUMO-protein ligase CBX4	Family
A, B	IPR017984	Chromo domain subgroup	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: O00257	attention deficit hyperactivity disorder, inattentive type breast carcinoma invasive ductal breast carcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm tuberculosis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ juvenile dermatomyositis osteosarcoma primitive neuroectodermal tumor ulcerative colitis breast cancer glioblastoma large cell medulloblastoma attention deficit hyperactivity disorder, inattentive type breast carcinoma invasive ductal breast carcinoma medulloblastoma pancreatic intraductal papillary-mucinous neoplasm tuberculosis atypical teratoid rhabdoid tumor ductal breast carcinoma in situ juvenile dermatomyositis osteosarcoma primitive neuroectodermal tumor ulcerative colitis breast cancer glioblastoma large cell medulloblastoma ovarian cancer rheumatoid arthritis

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.