3DM1

Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide

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	8062995	3000161	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Chromo domain-like	8062995	3000161	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Chromo domain-like	8062995	3000161	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Chromo domain-like	8062995	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	Chromo	e3dm1A1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
C	Chromo	e3dm1C1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
E	Chromo	e3dm1E1	A: beta barrels	X: SH3	H: Chromo domain-like (From Topology)	T: Chromo domain-like	F: Chromo	ECOD (1.6)
G	Chromo	e3dm1G1	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)
C	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
E	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)
G	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, C, E, G	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, C, E, G	Chromobox protein homolog 3	protein binding binding protein domain specific binding chromatin binding transcription factor binding transcription coregulator binding histone methyltransferase binding enzyme 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 cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process cellular biosynthetic process negative regulation of biological process RNA metabolic process negative regulation of cellular 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 cellular metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic 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 rhythmic process cellular component organization chromatin organization chromatin remodeling cellular component organization or biogenesis heterochromatin formation epigenetic regulation of gene expression negative regulation of gene expression negative regulation of gene expression, epigenetic	membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex membrane-bounded organelle intracellular organelle organelle envelope intracellular anatomical structure organelle nuclear envelope nucleus cellular anatomical entity intracellular membrane-bounded organelle endomembrane system RNA polymerase II transcription regulator complex protein-containing complex nuclear protein-containing complex transcription regulator complex intracellular non-membrane-bounded organelle chromosome, centromeric region chromosome chromosomal region non-membrane-bounded organelle chromatin silencing complex chromatin lock complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen chromatin pericentric heterochromatin heterochromatin organelle inner membrane nuclear membrane membrane nuclear inner membrane organelle membrane cytoskeleton spindle microtubule cytoskeleton condensed chromosome, centromeric region condensed chromosome euchromatin chromosome, telomeric region site of DNA damage
B, D, F, H	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3	p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity p53 binding protein binding binding transcription factor binding transcription coregulator binding transcription corepressor binding protein-lysine N-methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups lysine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity transferase activity methyltransferase activity catalytic activity S-adenosylmethionine-dependent methyltransferase activity histone H3 methyltransferase activity histone H3K56 methyltransferase activity histone methyltransferase activity histone modifying activity histone H3K9me2 methyltransferase activity histone H3K9 methyltransferase activity chromatin binding promoter-specific chromatin binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding organic cyclic compound binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding C2H2 zinc finger domain binding protein domain specific binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding histone H3K27 methyltransferase activity enzyme binding	developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate specification generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process neuron fate specification developmental process multicellular organismal process cellular developmental process neuron fate commitment nervous system development cell fate specification generation of neurons neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development cellular process neuron fate specification cell fate commitment system development adult behavior response to stimulus response to oxygen-containing compound response to nitrogen compound response to alkaloid behavior behavioral response to cocaine response to chemical response to organic cyclic compound response to cocaine regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of gene expression via chromosomal CpG island methylation negative regulation of cellular metabolic process cellular component organization chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression cellular metabolic process negative regulation of metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process developmental growth growth organ growth sexual reproduction reproductive process fertilization peptidyl-lysine methylation protein methylation peptidyl-lysine modification primary metabolic process macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-amino acid modification protein metabolic process protein modification process peptidyl-lysine dimethylation meiotic chromosome segregation synaptonemal complex assembly meiotic cell cycle process cellular component biogenesis cellular component assembly meiosis I meiotic nuclear division cell cycle synaptonemal complex organization chromosome segregation cell cycle process meiotic cell cycle organelle fission chromosome organization chromosome organization involved in meiotic cell cycle organelle organization nuclear division meiosis I cell cycle process homologous chromosome pairing at meiosis nuclear chromosome segregation homologous chromosome segregation DNA metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication regulation of nucleobase-containing compound metabolic process regulation of DNA replication regulation of DNA metabolic process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation gamete generation oocyte development germ cell development oocyte differentiation phenotypic switching DNA methylation-dependent heterochromatin formation heterochromatin formation constitutive heterochromatin formation response to alcohol response to ethanol system process learning or memory long-term memory nervous system process cognition memory regulation of protein modification process regulation of protein metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation spermatid development spermatid differentiation spermatogenesis male gamete generation response to antibiotic response to fungicide response to toxic substance cellular response to nitrogen compound cellular response to organic cyclic compound cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to cocaine cellular response to alkaloid negative regulation of cellular catabolic process catabolic process regulation of cellular component organization macroautophagy autophagy negative regulation of organelle assembly autophagosome organization regulation of autophagy cellular catabolic process process utilizing autophagic mechanism negative regulation of autophagosome assembly negative regulation of catabolic process autophagosome assembly organelle assembly vacuole organization negative regulation of cellular component organization regulation of autophagosome assembly regulation of vacuole organization regulation of catabolic process regulation of cellular component biogenesis regulation of organelle organization negative regulation of macroautophagy regulation of macroautophagy negative regulation of organelle organization negative regulation of autophagy regulation of organelle assembly regulation of cellular catabolic process cellular response to xenobiotic stimulus response to xenobiotic stimulus RNA metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle lumen nuclear speck nuclear body intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR023780	Chromo domain	Domain
A, C, E, G	IPR016197	Chromo-like domain superfamily	Homologous Superfamily
A, C, E, G	IPR023779	Chromo domain, conserved site	Conserved Site
A, C, E, G	IPR008251	Chromo shadow domain	Domain
A, C, E, G	IPR051219	Heterochromatin-associated chromo domain-containing protein	Family
A, C, E, G	IPR038033	Chromobox protein homologue 3, chromo domain	Domain
A, C, E, G	IPR000953	Chromo/chromo shadow domain	Domain
A, C, E, G	IPR017984	Chromo domain subgroup	Domain
B, D, F, H	IPR043550	Histone-lysine N-methyltransferase EHMT1/EHMT2	Family
B, D, F, H	IPR007728	Pre-SET domain	Domain
B, D, F, H	IPR046341	SET domain superfamily	Homologous Superfamily
B, D, F, H	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
B, D, F, H	IPR001214	SET domain	Domain
B, D, F, H	IPR038034	Histone-lysine N-methyltransferase EHMT2, SET domain	Domain
B, D, F, H	IPR047762	EHMT1/2, cysteine-rich region	Domain
B, D, F, H	IPR002110	Ankyrin repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C, E, G	Pharos: Q13185	myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor acute myeloid leukemia atypical teratoid rhabdoid tumor dermatomyositis gastric carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm myopathy osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma primitive neuroectodermal tumor acute myeloid leukemia atypical teratoid rhabdoid tumor dermatomyositis gastric carcinoma lung adenocarcinoma malignant ependymoma medulloblastoma nasopharyngeal carcinoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm plasma cell myeloma psoriasis adenoma breast cancer diabetes mellitus glioblastoma lung cancer malignant glioma metabolic syndrome X oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primary hyperoxaluria type 1 rheumatoid arthritis astrocytic tumor Crohn disease esophageal adenocarcinoma large cell medulloblastoma lymphoplasmacytic lymphoma malignant pancreatic neoplasm
B, D, F, H	Pharos: Q96KQ7	acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 squamous cell lung carcinoma age-related macular degeneration systemic lupus erythematosus vitiligo hepatitis B virus infection infertility disorder lung carcinoma acute myeloid leukemia cocaine abuse Neoplasm Metastasis vesicular stomatitis cocaine dependence lung cancer non-alcoholic fatty liver disease primary hyperoxaluria type 1 squamous cell lung carcinoma age-related macular degeneration systemic lupus erythematosus vitiligo hepatitis B virus infection infertility disorder lung carcinoma membranous glomerulonephritis osteosarcoma psoriatic arthritis ulcerative colitis wet macular degeneration endometriosis Hashimoto thyroiditis hypertensive disorder lung benign neoplasm ovarian cancer skin basal cell carcinoma autism spectrum disorder cervical cancer eosinophilic esophagitis heart disease

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H	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.