3I3C

Crystal Structural of CBX5 Chromo Shadow Domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3i3ca_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3i3cb_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3i3cc_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3i3cd_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01393	e3i3cA1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF01393	ECOD (1.6)
B	PF01393	e3i3cB1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF01393	ECOD (1.6)
C	PF01393	e3i3cC1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF01393	ECOD (1.6)
D	PF01393	e3i3cD1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: PF01393	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)
C	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
D	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, C, D	PF01393	Chromo shadow domain (Chromo_shadow)	Chromo shadow domain	This domain is distantly related to Pfam:PF00385. This domain is always found in association with a chromo domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Chromobox protein homolog 5	histone deacetylase binding protein binding binding enzyme binding protein-containing complex binding chromatin binding ribonucleoprotein complex binding protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding DNA-binding transcription factor binding methylated histone binding modification-dependent protein binding histone binding histone deacetylase binding protein binding binding enzyme binding protein-containing complex binding chromatin binding ribonucleoprotein complex binding protein-macromolecule adaptor activity molecular adaptor activity transcription factor binding DNA-binding transcription factor binding methylated histone binding modification-dependent protein binding histone binding methylation-dependent protein binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II protein-DNA complex organization cellular component organization protein-containing complex organization chromatin organization cellular component organization or biogenesis	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 organelle envelope nuclear envelope endomembrane system protein-containing complex histone methyltransferase complex catalytic complex nuclear protein-containing complex transferase complex nucleoplasm methyltransferase complex pericentric heterochromatin protein-DNA complex chromatin chromosome heterochromatin chromosomal region chromosome, centromeric region kinetochore condensed chromosome, centromeric region supramolecular complex condensed chromosome chromocenter histone deacetylase complex transcription regulator complex transcription repressor complex ribonucleoprotein complex chromosome, telomeric region site of DNA damage

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR023780	Chromo domain	Domain
A, B, C, D	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR023779	Chromo domain, conserved site	Conserved Site
A, B, C, D	IPR008251	Chromo shadow domain	Domain
A, B, C, D	IPR000953	Chromo/chromo shadow domain	Domain
A, B, C, D	IPR017984	Chromo domain subgroup	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P45973	colorectal cancer osteosarcoma primary hyperoxaluria type 1 sarcoidosis acute myeloid leukemia astrocytic tumor cystic fibrosis large cell medulloblastoma malignant ependymoma myocardial infarction ovarian cancer primitive neuroectodermal tumor adrenal cortex carcinoma atrial fibrillation colorectal carcinoma colorectal cancer osteosarcoma primary hyperoxaluria type 1 sarcoidosis acute myeloid leukemia astrocytic tumor cystic fibrosis large cell medulloblastoma malignant ependymoma myocardial infarction ovarian cancer primitive neuroectodermal tumor adrenal cortex carcinoma atrial fibrillation colorectal carcinoma glioblastoma lung adenocarcinoma malignant glioma oligodendroglioma Pick disease rheumatoid arthritis Alzheimer disease atypical teratoid rhabdoid tumor Colorectal Neoplasms heart disease lung carcinoma medulloblastoma

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.