3H91 | pdb_00003h91

Crystal structure of the complex of human chromobox homolog 2 (CBX2) and H3K27 peptide

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3h91b_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3h91a_	All beta proteins	SH3-like barrel	Chromo domain-like	Chromo domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Chromo domain-like	8066171	3000161	SCOP2B (2022-06-29)
A	SCOP2 Family	Chromo domain	8066170	4000375	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Chromo domain-like	8066171	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)
B	Chromo	e3h91B1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
A	Chromo	e3h91A1	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)
B	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
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, 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
C, D	H3K27 peptide	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	protein-containing complex intracellular anatomical structure protein-DNA complex nucleosome intracellular membraneless organelle chromatin chromosome intracellular organelle cellular anatomical structure organelle membraneless organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, B	Chromobox protein homolog 2	DNA binding binding nucleic acid binding histone H3K9me2/3 reader activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding	developmental process multicellular organism development multicellular organismal process development of primary sexual characteristics reproductive process sex differentiation anatomical structure development developmental process involved in reproduction cellular developmental process cell differentiation cellular process regulation of cellular process negative regulation of biological process RNA metabolic process developmental process multicellular organism development multicellular organismal process development of primary sexual characteristics reproductive process sex differentiation anatomical structure development developmental process involved in reproduction cellular developmental process cell differentiation cellular 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 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	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 membraneless organelle intracellular membraneless organelle chromatin chromosome 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 membraneless organelle intracellular membraneless organelle chromatin chromosome heterochromatin PRC1 complex ubiquitin ligase complex catalytic complex transferase complex nuclear ubiquitin ligase complex intracellular protein-containing complex euchromatin membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR000164	Histone H3/CENP-A	Family
C, D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
A, B	IPR000953	Chromo/chromo shadow domain	Domain
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	IPR042796	Chromobox protein homolog 2	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q14781	46,XY complete gonadal dysgenesis 46,XY sex reversal 5 atypical teratoid rhabdoid tumor Disorders of Sex Development gonadal dysgenesis malignant ependymoma non-small cell lung carcinoma psoriasis breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma malignant glioma ovarian cancer attention deficit hyperactivity disorder, inattentive type breast carcinoma 46,XY complete gonadal dysgenesis 46,XY sex reversal 5 atypical teratoid rhabdoid tumor Disorders of Sex Development gonadal dysgenesis malignant ependymoma non-small cell lung carcinoma psoriasis breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma malignant glioma ovarian cancer attention deficit hyperactivity disorder, inattentive type breast carcinoma glioblastoma large cell medulloblastoma medulloblastoma primitive neuroectodermal tumor

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	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.