3dm1

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

Method: X-RAY DIFFRACTION D_max: 65.0 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromobox protein homolog 3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 29–86	Fragment：Chromo 1 domain: Residues 29-86	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 29–86	Fragment：Chromo 1 domain: Residues 29-86	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 29–86	Fragment：Chromo 1 domain: Residues 29-86	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 29–86	Fragment：Chromo 1 domain: Residues 29-86	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 1 （Q96KQ7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
5	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 29–86 Chain C； UniProt 29–86 Chain E； UniProt 29–86 Chain G； UniProt 29–86	Fragment：Chromo 1 domain: Residues 29-86	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3 × 4 （Q96KQ7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3DM1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2L11 Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide Deposited 2010-07-22	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–81（53 aa） Fragment：UNP Residues 29-81	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 200；Pressure ambient NMR sample composition 20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.5 mM PMSF, 1 mM Benzamidine, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3KUP Crystal Structure of the CBX3 Chromo Shadow Domain Deposited 2009-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173) Chain B 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173)	Not recorded	UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.261
3KUP Crystal Structure of the CBX3 Chromo Shadow Domain Deposited 2009-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173) Chain D 110–173（64 aa） Fragment：Chromo Shadow Domain (UNP residues 110-173)	Not recorded	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% PEG1500, 0.2M sodium chloride, 0.1M HEPES, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.77 Å R-free 0.261
3TZD Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3) Deposited 2011-09-27	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 29–81（53 aa） Fragment：UNP residues 29-81	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；peg, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 1.81 Å R-free 0.231
5T1I CBX3 chromo shadow domain in complex with histone H3 peptide Deposited 2016-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 110–176（67 aa） Fragment：unp residues 110-176 Chain B 110–176（67 aa） Fragment：unp residues 110-176	Not recorded	UNX UNKNOWN LIGAND × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG 3350, 0.2 M sodium chloride, 0.1 M Hepes, 5% Ethylene Glycol	Resolution 1.60 Å R-free 0.239
6HW2 The Crystal Structure of CaV beta4c in complex with HP1gamma chromo shadow domains Deposited 2018-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 109–183（75 aa） Chain C 109–183（75 aa）	Not recorded	CA CALCIUM ION × 4 GOL GLYCEROL × 1 BME BETA-MERCAPTOETHANOL × 5 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；292 K；0.15 M NaCl, 12-14% PEG 3350 , pH 5.0, calcium acetate, VAPOR DIFFUSION, temperature 292K	Resolution 1.94 Å R-free 0.209
9OSC Crystal structure of HP1gamma chromoshadow domain in complex with KAP1 peptide Deposited 2025-05-23	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–176（67 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；1.0 M LiCl2, 0.1 M citrate buffer pH 4.0, and 20% PEG6000	Resolution 1.77 Å R-free 0.236

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CBX3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–58； UniProt 29–86 Author chain C； PDBConstruct 1–58； UniProt 29–86 Author chain E； PDBConstruct 1–58； UniProt 29–86 Author chain G； PDBConstruct 1–58； UniProt 29–86

Histone-lysine N-methyltransferase, H3 lysine-9 specific 3

OrganismNot specified

UniProt Q96KQ7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 179–190	Fragment：UNP residues 179-190 Non-standard monomer：Yes (specific site not provided by mmCIF)	Chromobox protein homolog 3 × 1 （Q13185）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 179–190	Fragment：UNP residues 179-190 Non-standard monomer：Yes (specific site not provided by mmCIF)	Chromobox protein homolog 3 × 1 （Q13185）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 179–190	Fragment：UNP residues 179-190 Non-standard monomer：Yes (specific site not provided by mmCIF)	Chromobox protein homolog 3 × 1 （Q13185）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 179–190	Fragment：UNP residues 179-190 Non-standard monomer：Yes (specific site not provided by mmCIF)	Chromobox protein homolog 3 × 1 （Q13185）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267
5	Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain B； UniProt 179–190 Chain D； UniProt 179–190 Chain F； UniProt 179–190 Chain H； UniProt 179–190	Fragment：UNP residues 179-190 Non-standard monomer：Yes (specific site not provided by mmCIF)	Chromobox protein homolog 3 × 4 （Q13185）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；1.5 microliter of the protein solution mixed with with 1.5 microliter of the reservoir solution containing 40% PEG 550 MME, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.267

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3DM1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2O8J Human euchromatic histone methyltransferase 2 Deposited 2006-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；peg 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.221
2O8J Human euchromatic histone methyltransferase 2 Deposited 2006-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；peg 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.221
2O8J Human euchromatic histone methyltransferase 2 Deposited 2006-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；peg 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.221
2O8J Human euchromatic histone methyltransferase 2 Deposited 2006-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；peg 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.80 Å R-free 0.221
3K5K Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a Deposited 2009-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 913–1193（281 aa） Fragment：UNP residues 913-1193, SET domain	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 DXQ 7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine × 1 CL CHLORIDE ION × 2 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.2M sodium fluoride, 0.1M Bis-Tris phosphate pH 6.0, 18% polyethylene glycol 3350 and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.264
3K5K Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a Deposited 2009-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 913–1193（281 aa） Fragment：UNP residues 913-1193, SET domain	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 DXQ 7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine × 1 CL CHLORIDE ION × 2 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.2M sodium fluoride, 0.1M Bis-Tris phosphate pH 6.0, 18% polyethylene glycol 3350 and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.264
3K5K Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent Inhibitor of Histone Lysine Methyltransferase, G9a Deposited 2009-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Fragment：UNP residues 913-1193, SET domain Chain B 913–1193（281 aa） Fragment：UNP residues 913-1193, SET domain	Not recorded	ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 DXQ 7-[3-(dimethylamino)propoxy]-6-methoxy-2-(4-methyl-1,4-diazepan-1-yl)-N-(1-methylpiperidin-4-yl)quinazolin-4-amine × 2 CL CHLORIDE ION × 4 UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.2M sodium fluoride, 0.1M Bis-Tris phosphate pH 6.0, 18% polyethylene glycol 3350 and 10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.264
3RJW Crystal structure of histone lysine methyltransferase g9a with an inhibitor Deposited 2011-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Fragment：Sequence database residues 913-1193 Chain B 913–1193（281 aa） Fragment：Sequence database residues 913-1193	Not recorded	ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 CIQ 2-cyclohexyl-6-methoxy-N-[1-(1-methylethyl)piperidin-4-yl]-7-(3-pyrrolidin-1-ylpropoxy)quinazolin-4-amine × 2 UNX UNKNOWN LIGAND × 29	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；291 K；0.2M SODIUM FORMATE, 10% ETHYLENE GLYCOL, 25% PEG-3350, 0.1M BIS-TRIS PROPANE, pH 6.5, vapor diffusion, temperature 291K	Resolution 2.56 Å R-free 0.245
4NVQ Human G9a in Complex with Inhibitor A-366 Deposited 2013-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	2OD 5'-methoxy-6'-[3-(pyrrolidin-1-yl)propoxy]spiro[cyclobutane-1,3'-indol]-2'-amine × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.75；277 K；0.1 M BIS-TRIS, 17.0% PEG3350, pH 5.75, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.03 Å R-free 0.239
5JHN Structure of G9a SET-domain with Histone H3K9Ala mutant peptide and bound S-adenosylmethionine Deposited 2016-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 882–1155（274 aa） Fragment：UNP residues 882-1155 Chain B 882–1155（274 aa） Fragment：UNP residues 882-1155	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350	Resolution 1.67 Å R-free 0.237
5JIN Structure of G9a SET-domain with Histone H3K9M mutant peptide and bound S-adenosylmethionine Deposited 2016-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 882–1155（274 aa） Fragment：UNP residues 882-1155 Chain B 882–1155（274 aa） Fragment：UNP residues 882-1155	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；298 K；0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350	Resolution 1.85 Å R-free 0.240
5JIY Structure of G9a SET-domain with Histone H3K9norLeucine mutant peptide and bound S-adenosylmethionine Deposited 2016-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 882–1155（274 aa） Fragment：UNP residues 882-1155 Chain B 882–1155（274 aa） Fragment：UNP residues 882-1155	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350	Resolution 1.48 Å R-free 0.233
5JJ0 Structure of G9a SET-domain with Histone H3K9M peptide and excess SAH Deposited 2016-04-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 882–1155（274 aa） Fragment：SET domain of Histone-lysine N-methyltransferase EHMT2 G9a, UNP residues 882-1155 Chain B 882–1155（274 aa） Fragment：SET domain of Histone-lysine N-methyltransferase EHMT2 G9a, UNP residues 882-1155	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2 M Tri-ammonium citrate pH 7 and 20% w/v polyethylene glycol 3350	Resolution 1.72 Å R-free 0.252
5T0K Structure of G9a SET-domain with H3K9M mutant peptide and SAM Deposited 2016-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 879–1159（281 aa）	Not recorded	ZN ZINC ION × 4 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol	Resolution 1.70 Å R-free 0.193
5T0K Structure of G9a SET-domain with H3K9M mutant peptide and SAM Deposited 2016-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 879–1159（281 aa）	Not recorded	ZN ZINC ION × 4 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol	Resolution 1.70 Å R-free 0.193
5T0M A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading Deposited 2016-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 879–1159（281 aa） Fragment：unp residues 879-1159	Not recorded	ZN ZINC ION × 4 SAM S-ADENOSYLMETHIONINE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol	Resolution 1.90 Å R-free 0.224
5T0M A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading Deposited 2016-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 879–1159（281 aa） Fragment：unp residues 879-1159	Not recorded	ZN ZINC ION × 4 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1 M Bis-Tris propane (pH 7.5), 18% (w/v) PEG3350, 0.2 M NaF, and 5% (v/v) ethylene glycol	Resolution 1.90 Å R-free 0.224
5TTF Crystal structure of catalytic domain of G9a with MS012 Deposited 2016-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 879–1159（281 aa） Fragment：UNP residues 879-1159 Chain C 879–1159（281 aa） Fragment：UNP residues 879-1159	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 7KZ N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine × 2 CL CHLORIDE ION × 1 UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5	Resolution 1.72 Å R-free 0.247
5TTF Crystal structure of catalytic domain of G9a with MS012 Deposited 2016-11-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 879–1159（281 aa） Fragment：UNP residues 879-1159 Chain D 879–1159（281 aa） Fragment：UNP residues 879-1159	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 7KZ N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine × 2 UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5	Resolution 1.72 Å R-free 0.247
5TUY Structure of human G9a SET-domain (EHMT2) in complex with inhibitor MS0124 Deposited 2016-11-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 887–1154（268 aa） Fragment：UNP residues 887-1154 Chain B 887–1154（268 aa） Fragment：UNP residues 887-1154	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 7L6 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；290 K；20% (w/v) PEG 3,350, 0.2 M NaF, 0.1 M Bis-Tris propane (pH 6.5)	Resolution 2.60 Å R-free 0.234
5V9I Crystal structure of catalytic domain of G9a with MS0105 Deposited 2017-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Fragment：residues 913-1193 Chain B 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 90P N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine × 2 GOL GLYCEROL × 6 UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5	Resolution 1.74 Å R-free 0.275
5V9I Crystal structure of catalytic domain of G9a with MS0105 Deposited 2017-03-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 913–1193（281 aa） Fragment：residues 913-1193 Chain D 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 90P N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine × 2 GOL GLYCEROL × 3 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH6.5	Resolution 1.74 Å R-free 0.275
5VSC Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 13 Deposited 2017-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 916–1190（275 aa） Fragment：G9a catalytic SET-domain residues 916-1190 Chain B 916–1190（275 aa） Fragment：G9a catalytic SET-domain residues 916-1190	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 9HJ 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；290 K；20 % PEG3350, 10% glycerol, 0.2 M Sodium bromide	Resolution 1.40 Å R-free 0.182
5VSE Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine Deposited 2017-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 883–1156（274 aa） Fragment：G9a catalytic SET-domain (913-1193)	Not recorded	ZN ZINC ION × 4 SAM S-ADENOSYLMETHIONINE × 1 9HG N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；290 K；20 % PEG3350, 10% glycerol, 0.2 M Sodium fluoride, Bis-Tris propane pH6.5	Resolution 1.60 Å R-free 0.191
5VSE Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine Deposited 2017-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 883–1156（274 aa） Fragment：G9a catalytic SET-domain (913-1193)	Not recorded	ZN ZINC ION × 4 SAM S-ADENOSYLMETHIONINE × 1 9HG N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；290 K；20 % PEG3350, 10% glycerol, 0.2 M Sodium fluoride, Bis-Tris propane pH6.5	Resolution 1.60 Å R-free 0.191
5VSE Structure of human G9a SET-domain (EHMT2) in complex with inhibitor 17: N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine Deposited 2017-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 883–1156（274 aa） Fragment：G9a catalytic SET-domain (913-1193) Chain B 883–1156（274 aa） Fragment：G9a catalytic SET-domain (913-1193)	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 9HG N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；290 K；20 % PEG3350, 10% glycerol, 0.2 M Sodium fluoride, Bis-Tris propane pH6.5	Resolution 1.60 Å R-free 0.191
6MM1 Structure of the cysteine-rich region from human EHMT2 Deposited 2018-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 419–552（134 aa） Fragment：residues 419-552	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M potassium sodium tartrate 18% PEG 3350 0.1M HEPES, pH 8.0	Resolution 1.90 Å R-free 0.223
6MM1 Structure of the cysteine-rich region from human EHMT2 Deposited 2018-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 419–552（134 aa） Fragment：residues 419-552	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M potassium sodium tartrate 18% PEG 3350 0.1M HEPES, pH 8.0	Resolution 1.90 Å R-free 0.223
6MM1 Structure of the cysteine-rich region from human EHMT2 Deposited 2018-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 419–552（134 aa） Fragment：residues 419-552	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M potassium sodium tartrate 18% PEG 3350 0.1M HEPES, pH 8.0	Resolution 1.90 Å R-free 0.223
6MM1 Structure of the cysteine-rich region from human EHMT2 Deposited 2018-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 419–552（134 aa） Fragment：residues 419-552	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2M potassium sodium tartrate 18% PEG 3350 0.1M HEPES, pH 8.0	Resolution 1.90 Å R-free 0.223
7BTV Crystal structure of EHMT2 SET domain in complex with compound 5. Deposited 2020-04-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 N47 N~2~-{4-methoxy-3-[3-(pyrrolidin-1-yl)propoxy]phenyl}-N~4~,6-dimethylpyrimidine-2,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium acetate, 20% PEG 3350	Resolution 2.00 Å R-free 0.245
7BUC Crystal structure of EHMT2 SET domain in complex with compound 13 Deposited 2020-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 F80 N2-[4-methoxy-3-(2,3,4,7-tetrahydro-1H-azepin-5-yl)phenyl]-N4,6-dimethyl-pyrimidine-2,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M magnesium acetate, 20% polyethyleneglycol 3350	Resolution 2.60 Å R-free 0.262
7DCF Crystal structure of EHMT2 SET domain in complex with compound 10 Deposited 2020-10-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 H30 5'-methoxy-6'-(1-methyl-2,3,4,7-tetrahydroazepin-5-yl)spiro[cyclobutane-1,3'-indole]-2'-amine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M NaOAc, pH 7, 20% PEG 3350	Resolution 1.80 Å R-free 0.246
7T7L Structure of human G9a SET-domain (EHMT2) in complex with covalent inhibitor (Compound 1) Deposited 2021-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Fragment：residues 913-1193 Chain C 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 G5U N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)propanamide × 1 G4R N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)prop-2-enamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；2% v/v 1,4-Dioxane, 10% w/v Polyethylene glycol 20,000	Resolution 2.20 Å R-free 0.251
7T7L Structure of human G9a SET-domain (EHMT2) in complex with covalent inhibitor (Compound 1) Deposited 2021-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 913–1193（281 aa） Fragment：residues 913-1193 Chain D 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 G5U N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)propanamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；2% v/v 1,4-Dioxane, 10% w/v Polyethylene glycol 20,000	Resolution 2.20 Å R-free 0.251
7X73 Structure of G9a in complex with RK-701 Deposited 2022-03-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 J26 N-[(2S)-1-[(4-cyanophenyl)amino]-4-cyclopropyl-1-oxidanylidene-butan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1H-indole-2-carboxamide × 2 EDO 1,2-ETHANEDIOL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1M Bis-Tris propane (pH 7.4), 0.2M sodium formate, 10% ethylene glycol, 25% PEG3350	Resolution 1.49 Å R-free 0.193
7XUA Structure of G9a in complex with compound 10a Deposited 2022-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 I5X ~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)-3-methylsulfanyl-propyl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH7.5), 0.2M Sodium Formate, 10% Ethylene Glycol, 23.5% PEG3350	Resolution 1.87 Å R-free 0.224
7XUB Structure of G9a in complex with compound 10d Deposited 2022-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 I6L ~{N}-[(1~{S})-1-(1~{H}-benzimidazol-2-yl)pentyl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide × 2 EDO 1,2-ETHANEDIOL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (7.75), 0.2M Sodium Formate, 10% Ethylene Glycol, 26% PEG3350	Resolution 2.00 Å R-free 0.215
7XUC Structure of G9a in complex with compound 11a Deposited 2022-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 I6S 3,6,6-trimethyl-4-oxidanylidene-~{N}-[(2~{S})-1-oxidanylidene-1-phenylazanyl-hexan-2-yl]-5,7-dihydro-1~{H}-indole-2-carboxamide × 2 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH7.5), 0.2M Sodium Fluoride, 10% Ethylene Glycol, 25% PEG3350	Resolution 1.67 Å R-free 0.186
7XUD Structure of G9a in complex with compound 26a Deposited 2022-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 CL CHLORIDE ION × 1 SFG SINEFUNGIN × 2 I6Z ~{N}-[(2~{S})-4-cyclopropyl-1-oxidanylidene-1-phenylazanyl-butan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide × 2 EDO 1,2-ETHANEDIOL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH7.5), 0.2M Sodium Fluoride, 10% Ethylene Glycol, 22% PEG3350	Resolution 1.45 Å R-free 0.177
8VV8 Crystal Structure of EHMT2 bound to EZM8266 Deposited 2024-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 A1AEB (2R)-1-(azetidin-1-yl)-3-(2-methoxy-5-{[4-methyl-6-(methylamino)pyrimidin-2-yl]amino}phenoxy)propan-2-ol × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium fluoride, 20 %(w/v) PEG 3350	Resolution 2.00 Å R-free 0.247
8VV8 Crystal Structure of EHMT2 bound to EZM8266 Deposited 2024-01-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 913–1193（281 aa） Fragment：residues 913-1193	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 A1AEB (2R)-1-(azetidin-1-yl)-3-(2-methoxy-5-{[4-methyl-6-(methylamino)pyrimidin-2-yl]amino}phenoxy)propan-2-ol × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M Potassium fluoride, 20 %(w/v) PEG 3350	Resolution 2.00 Å R-free 0.247
8Z7C Structure of G9a in complex with compound 7i Deposited 2024-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 A1L07 3,6,6-trimethyl-~{N}-[(2~{S})-1-[[4-(1-methylpiperidin-4-yl)oxyphenyl]amino]-1-oxidanylidene-hexan-2-yl]-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH~7.5), 0.2M Sodium Formate or Fluoride, 10% Ethylene Glycol, ~25% PEG3350	Resolution 1.52 Å R-free 0.196
8Z7D Structure of G9a in complex with compound 9a Deposited 2024-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 A1L08 3,6,6-trimethyl-4-oxidanylidene-~{N}-[(2~{S})-1-oxidanylidene-1-[(phenylmethyl)amino]hexan-2-yl]-5,7-dihydro-1~{H}-indole-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH~7.5), 0.2M Sodium Formate or Fluoride, 10% Ethylene Glycol, ~25% PEG3350	Resolution 1.58 Å R-free 0.183
8Z7E Structure of G9a in complex with compound 9b Deposited 2024-04-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 A1L09 ~{N}-[(2~{S})-1-[[4-[(dimethylamino)methyl]phenyl]methylamino]-1-oxidanylidene-hexan-2-yl]-3,6,6-trimethyl-4-oxidanylidene-5,7-dihydro-1~{H}-indole-2-carboxamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH~7.5), 0.2M Sodium Formate or Fluoride, 10% Ethylene Glycol, ~25% PEG3350	Resolution 1.54 Å R-free 0.195
9KLB G9a in complex with RK-133232 (compound 16g) Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 A1L57 ~{N}-[(~{E},2~{S})-4-cyclopropyl-1-[(6-ethoxypyridin-3-yl)amino]-1-oxidanylidene-but-3-en-2-yl]-4-(pyridin-4-ylamino)benzamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH~7.5), 0.2M Sodium Formate or Fluoride, 10% Ethylene Glycol, ~25% PEG3350	Resolution 1.81 Å R-free 0.221
9KLC G9a in complex with the S-isomer of RK-131902 (racemic compound rac-10a) Deposited 2024-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2 A1L58 ~{N}-[(2~{S})-1-[[6-(1-methylpiperidin-4-yl)oxypyridin-3-yl]amino]-1-oxidanylidene-hexan-2-yl]-3-(pyridin-4-ylamino)benzamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Bis-Tris propane (pH~7.5), 0.2M Sodium Formate or Fluoride, 10% Ethylene Glycol, ~25% PEG3350	Resolution 2.15 Å R-free 0.253
9LUS Structure of human G9a SET-domain in complex with FLAV27 inhibitor Deposited 2025-02-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 913–1193（281 aa） Chain B 913–1193（281 aa）	Not recorded	ZN ZINC ION × 2 A1L7O 3-[1-[[(2~{S})-4-(phenylmethyl)-1,4-oxazepan-2-yl]methyl]piperidin-4-yl]phenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；peg3350 20%, 10% Tacsimate (ph-8), Tris (ph-8.2), Glycerol 6%, 5 mM KSCN	Resolution 2.70 Å R-free 0.309
9WRI Crystal structure of CtBP2 in complex with G9a Deposited 2025-09-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 881–893（13 aa）	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M HEPES pH 7.5, 6% PVP, 30% pentaerythritol ethoxylate	Resolution 1.85 Å R-free 0.202
9YKS Crystal structure of the G9a (EHMT2) SET domain in complex with SAM and TNG917 Deposited 2025-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 912–1193（282 aa） Fragment：catalytic SET domain (UNP residues 912-1193) Chain B 912–1193（282 aa） Fragment：catalytic SET domain (UNP residues 912-1193)	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 A1CXM N~2~-[(7M)-6-fluoro-7-(2,5,6,7-tetrahydro-1H-azepin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]-N~4~,6-dimethylpyrimidine-2,4-diamine × 2 EDO 1,2-ETHANEDIOL × 7 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；33% PEG4000, 200 mM sodium acetate, 100 mM MES, pH 6.5	Resolution 1.79 Å R-free 0.252
9YKS Crystal structure of the G9a (EHMT2) SET domain in complex with SAM and TNG917 Deposited 2025-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 912–1193（282 aa） Fragment：catalytic SET domain (UNP residues 912-1193) Chain D 912–1193（282 aa） Fragment：catalytic SET domain (UNP residues 912-1193)	Not recorded	ZN ZINC ION × 8 SAM S-ADENOSYLMETHIONINE × 2 A1CXM N~2~-[(7M)-6-fluoro-7-(2,5,6,7-tetrahydro-1H-azepin-4-yl)-2,3-dihydro-1-benzofuran-5-yl]-N~4~,6-dimethylpyrimidine-2,4-diamine × 2 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；33% PEG4000, 200 mM sodium acetate, 100 mM MES, pH 6.5	Resolution 1.79 Å R-free 0.252

34 other PDB entries and 51 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EHMT2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–12； UniProt 179–190 Author chain D； PDBConstruct 1–12； UniProt 179–190 Author chain F； PDBConstruct 1–12； UniProt 179–190 Author chain H； PDBConstruct 1–12； UniProt 179–190

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3dm1
Deposition date deposition_date	2008-06-30
Structure title title	Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide
Keywords keywords	;Chromobox homolog 3, Structural Genomics, Structural Genomics Consortium, SGC, Chromatin regulator, Nucleus, Phosphoprotein, Repressor, Transcription, Transcription regulation ;; TRANSCRIPTION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.34 Å
Radius of gyration Rg (electron density) rg_electron	19.51 Å
Forward intensity I(0) i0	13941000.00
Molecular weight molecular_weight	28410.0 kDa
Excluded volume excluded_volume	35708 Å³
Envelope volume envelope_volume	42994 Å³
Hydration-shell volume shell_volume	18767 Å³
Envelope diameter envelope_diameter	64.3 Å
Shell Rg shell_rg	25.34 Å
Envelope Rg envelope_rg	19.59 Å
Shape Rg shape_rg	19.51 Å
Total Rg total_rg	20.37 Å
Total atoms total_atoms	2010
Residues n_residues	240
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.0 Å
Rg (real space) rg_real	20.24 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	1.3940e+07
I(0) uncertainty (real space) i0_real_error	1.6910e+05
Rg (reciprocal space) rg_reciprocal	20.26 Å
I(0) (reciprocal space) i0_reciprocal	13940000.0000
Solution quality estimate total_estimate	0.8984
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.137
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3771000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Chromobox protein homolog 3
Molecular weight formula_weight	6812.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	2109

EFVVEKVLDRRVVNGKVEYFLKWKGFTDADNTWEPEENLDCPELIEAFLNSQKAGKEK

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone-lysine N-methyltransferase, H3 lysine-9 specific 3
Molecular weight formula_weight	1486.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

KVHRARKTMSKP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3dm1A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3dm1C00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3dm1E00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3dm1G00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	83.671 Å
Unit-cell length b length_b	83.671 Å
Unit-cell length c length_c	110.288 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	39.100 Å
R factor r_factor	0.2219
R_work r_work	0.2195
R_free r_free	0.2672

fit	/app/data/saxs_computation/dm/3dm1/3dm1.fit
pddf	/app/data/pr_computation/dm/3dm1/3dm1.pr.out
profile	/app/data/saxs_computation/dm/3dm1/3dm1.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromobox protein homolog 3

State in the Current Structure

Other States of the Same Protein in the Database

Histone-lysine N-methyltransferase, H3 lysine-9 specific 3

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)