3swc

GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide

Method: X-RAY DIFFRACTION D_max: 85.0 Å Quality: GOOD

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

Histone-lysine N-methyltransferase EHMT1

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 982–1266	Fragment：unp residues 982-1266	DNA (cytosine-5)-methyltransferase 3A × 1 （O88508） ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.227
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 982–1266	Fragment：unp residues 982-1266	DNA (cytosine-5)-methyltransferase 3A × 1 （O88508） ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.227
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 982–1266 Chain B； UniProt 982–1266	Fragment：unp residues 982-1266	DNA (cytosine-5)-methyltransferase 3A × 2 （O88508） ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.227

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 3SWC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IGQ Human euchromatic histone methyltransferase 1 Deposited 2006-09-23	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 951–1235（285 aa） Fragment：C-terminal domain, residues 951-1235 Chain B 951–1235（285 aa） Fragment：C-terminal domain, residues 951-1235	Not recorded	ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；20% PEG 4K, 10% Isoproponol, 0.1M Hepes 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.00 Å R-free 0.237
2RFI Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide Deposited 2007-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 951–1235（285 aa） Fragment：Catalytic domain: Residues 951-1235	Not recorded	ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.59 Å R-free 0.220
2RFI Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide Deposited 2007-09-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 951–1235（285 aa） Fragment：Catalytic domain: Residues 951-1235	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.59 Å R-free 0.220
2RFI Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and dimethylated H3K9 peptide Deposited 2007-09-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 951–1235（285 aa） Fragment：Catalytic domain: Residues 951-1235 Chain B 951–1235（285 aa） Fragment：Catalytic domain: Residues 951-1235	Not recorded	ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；300 K；16% PEG 4000, 10% Isopropanol, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.59 Å R-free 0.220
3B7B EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1) Deposited 2007-10-30	Different construct 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 734–968（235 aa） Fragment：Ankyrin repeat domains 2-7	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；1.5-2.0 M Lithium Sulfate, 1-4% Peg 400 or 550, 0.1 M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.99 Å R-free 0.261
3B7B EuHMT1 (Glp) Ankyrin Repeat Domain (Structure 1) Deposited 2007-10-30	Different construct 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 734–968（235 aa） Fragment：Ankyrin repeat domains 2-7	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；1.5-2.0 M Lithium Sulfate, 1-4% Peg 400 or 550, 0.1 M Tris buffer pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.99 Å R-free 0.261
3FPD G9a-like protein lysine methyltransferase inhibition by BIX-01294 Deposited 2009-01-05	Different construct 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 975–1235（261 aa） Fragment：UNP residues 975-1235, SET domain Chain B 975–1235（261 aa） Fragment：UNP residues 975-1235, SET domain	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 Q4A N-(1-benzylpiperidin-4-yl)-6,7-dimethoxy-2-(4-methyl-1,4-diazepan-1-yl)quinazolin-4-amine × 2 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；0.1 M HEPES pH 7.5, 18-20 % polyethylene glycol 4000 and 7-10 % isopropanol, in the absence or presence of DMSO (6-36%), VAPOR DIFFUSION, temperature 289K	Resolution 2.40 Å R-free 0.262
3HNA Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide Deposited 2009-05-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 951–1235（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；300 K；20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.50 Å R-free 0.193
3HNA Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide Deposited 2009-05-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 951–1235（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；300 K；20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.50 Å R-free 0.193
3HNA Crystal structure of catalytic domain of human euchromatic histone methyltransferase 1 in complex with SAH and mono-Methylated H3K9 Peptide Deposited 2009-05-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 951–1235（285 aa） Chain B 951–1235（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；300 K；20%PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 1.50 Å R-free 0.193
3MO0 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 2 ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.78 Å R-free 0.306
3MO0 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.78 Å R-free 0.306
3MO0 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E11 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain Chain B 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 3 ZN ZINC ION × 10 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M HEPES, 18 20% (v/v) polyethylene glycol 4000 and 7 10% (v/v) isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.78 Å R-free 0.306
3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.248
3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.248
3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.248
3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.248
3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 951–1235（285 aa） Fragment：C-terminal SET domain Chain B 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 8 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.248
3MO2 human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E67 Deposited 2010-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 951–1235（285 aa） Fragment：C-terminal SET domain Chain D 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 8 E67 7-[(5-aminopentyl)oxy]-N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.49 Å R-free 0.248
3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.14 Å R-free 0.233
3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.14 Å R-free 0.233
3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.14 Å R-free 0.233
3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22	Different construct 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 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 4 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.14 Å R-free 0.233
3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 951–1235（285 aa） Fragment：C-terminal SET domain Chain B 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 8 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.14 Å R-free 0.233
3MO5 Human G9a-like (GLP, also known as EHMT1) in complex with inhibitor E72 Deposited 2010-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 951–1235（285 aa） Fragment：C-terminal SET domain Chain D 951–1235（285 aa） Fragment：C-terminal SET domain	Not recorded	ZN ZINC ION × 8 E72 7-[(5-aminopentyl)oxy]-N~4~-[1-(5-aminopentyl)piperidin-4-yl]-N~2~-[3-(dimethylamino)propyl]-6-methoxyquinazoline-2,4-diamine × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes pH 7.5, 14% polyethylene glycol 4000, 9% isopropanol, and 12% dimethyl sulfoxide, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.14 Å R-free 0.233
3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 982–1266（285 aa） Fragment：unp residues 982-1266	Not recorded	ZN ZINC ION × 4 SFG SINEFUNGIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.05 Å R-free 0.248
3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 982–1266（285 aa） Fragment：unp residues 982-1266	Not recorded	ZN ZINC ION × 4 SFG SINEFUNGIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.05 Å R-free 0.248
3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13	Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 982–1266（285 aa） Fragment：unp residues 982-1266 Chain B 982–1266（285 aa） Fragment：unp residues 982-1266	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.05 Å R-free 0.248
4I51 Methyltransferase domain of HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, mutant Y1211A Deposited 2012-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 982–1266（285 aa） Chain B 982–1266（285 aa）	Mutation：Y1211A Mutation：Y1211A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 GOL GLYCEROL × 3 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；10% ISOPROPANOL, 20% PEG4000; 0.1M HEPES PH7.5, VAPOR DIFFUSION HANGING DROP, TEMPERATURE 297K	Resolution 1.90 Å R-free 0.195
5TTG Crystal structure of catalytic domain of GLP with MS012 Deposited 2016-11-03	Different construct 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 982–1266（285 aa） Fragment：UNP residues 879-1159	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 7KZ N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 4 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6	Resolution 1.66 Å R-free 0.192
5TTG Crystal structure of catalytic domain of GLP with MS012 Deposited 2016-11-03	Different construct 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 982–1266（285 aa） Fragment：UNP residues 879-1159	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 7KZ N4-(1-methylpiperidin-4-yl)-N2-hexyl-6,7-dimethoxyquinazoline-2,4-diamine × 1 ZN ZINC ION × 4 UNX UNKNOWN LIGAND × 9 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6	Resolution 1.66 Å R-free 0.192
5TUZ Structure of human GLP SET-domain (EHMT1) in complex with inhibitor MS0124 Deposited 2016-11-07	Different construct 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 1006–1266（261 aa） Fragment：UNP residues 1006-1266 Chain B 1006–1266（261 aa） Fragment：UNP residues 1006-1266	Not recorded	SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 7L6 6,7-dimethoxy-N-(1-methylpiperidin-4-yl)-2-(morpholin-4-yl)quinazolin-4-amine × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；290 K；20% PEG 20,000, 2% (v/v) 1,4-Dioxane, 0.1 M Bicine (pH 9.0)	Resolution 1.95 Å R-free 0.201
5V9J Crystal structure of catalytic domain of GLP with MS0105 Deposited 2017-03-23	Different construct 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 982–1266（285 aa） Fragment：residues 982-1266 Chain B 982–1266（285 aa） Fragment：residues 982-1266	Not recorded	SAM S-ADENOSYLMETHIONINE × 2 90P N~2~-cyclohexyl-N~4~-(1-ethylpiperidin-4-yl)-6,7-dimethoxy-N~2~-methylquinazoline-2,4-diamine × 2 ZN ZINC ION × 8 CL CHLORIDE ION × 3 UNX UNKNOWN LIGAND × 13 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；20% PEG 4000, 20% IProp, 0.1 M NaCitrate pH5.6	Resolution 1.74 Å R-free 0.197
5VSD Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 13 Deposited 2017-05-11	Different construct 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 1006–1266（261 aa） Fragment：GLP catalytic SET-domain residues 1006-1266 Chain B 1006–1266（261 aa） Fragment：GLP catalytic SET-domain residues 1006-1266	Not recorded	SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 9HJ 6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)-N~2~-propylquinazoline-2,4-diamine × 2 DIO 1,4-DIETHYLENE DIOXIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；290 K；7 % PEG 20K, 1.4% v/v 1,4-Dioxane, 10% glycerol, 0.07 M Bicine, pH 9.0	Resolution 1.85 Å R-free 0.235
5VSF Structure of human GLP SET-domain (EHMT1) in complex with inhibitor 17 Deposited 2017-05-11	Different construct 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 1006–1266（261 aa） Fragment：GLP catalytic SET-domain residues 1006-1266 Chain B 1006–1266（261 aa） Fragment：GLP catalytic SET-domain residues 1006-1266	Not recorded	SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 8 9HG N~2~-cyclopentyl-6,7-dimethoxy-N~2~-methyl-N~4~-(1-methylpiperidin-4-yl)quinazoline-2,4-diamine × 2 DIO 1,4-DIETHYLENE DIOXIDE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 9；290 K；10 % PEG 20K, 1.4% v/v 1,4-Dioxane, 10% glycerol, 0 0.1 M Bicine, pH 9.0	Resolution 1.70 Å R-free 0.185
6BY9 Crystal structure of EHMT1 Deposited 2017-12-20	Different construct 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 672–999（328 aa）	Not recorded	UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M BIS-TRIS pH6.5,3.0M NaCl	Resolution 2.30 Å R-free 0.238
6MBO GLP Methyltransferase with Inhibitor EML741-P212121 Crystal Form Deposited 2018-08-30	Different construct 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 1006–1266（261 aa） Chain B 1006–1266（261 aa）	Not recorded	JDG 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine × 4 ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 EDO 1,2-ETHANEDIOL × 14	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；15% PEG 4000, 20% isopropanol and 100mM citrate (pH 5.5)	Resolution 1.59 Å R-free 0.194
6MBP GLP Methyltransferase with Inhibitor EML741- P3121 Crystal Form Deposited 2018-08-30	Different construct 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 1006–1266（261 aa） Fragment：residues 1006-1266 Chain B 1006–1266（261 aa） Fragment：residues 1006-1266	Not recorded	JDG 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine × 2 ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；292 K；15% PEG 4000, 20% isopropanol and 100mM citrate (pH 5.5)	Resolution 1.95 Å R-free 0.182
7T7M Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1) Deposited 2021-12-15	Different construct 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 982–1266（285 aa） Fragment：residues 982-1266 Chain D 982–1266（285 aa） Fragment：residues 982-1266	Not recorded	ZN ZINC ION × 8 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 G5U N-(6-methoxy-4-{[1-(propan-2-yl)piperidin-4-yl]amino}-7-[3-(pyrrolidin-1-yl)propoxy]quinazolin-2-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；0.2 Magnesium Formate, 15% w/v Polyethylene glycol 3350	Resolution 2.85 Å R-free 0.244
7T7M Structure of human GLP SET-domain (EHMT1) in complex with covalent inhibitor (Compound 1) Deposited 2021-12-15	Different construct 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 982–1266（285 aa） Fragment：residues 982-1266 Chain C 982–1266（285 aa） Fragment：residues 982-1266	Not recorded	ZN ZINC ION × 8 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 × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290.15 K；0.2 Magnesium Formate, 15% w/v Polyethylene glycol 3350	Resolution 2.85 Å R-free 0.244
8XPT The Crystal Structure of EHMT1 from Biortus. Deposited 2024-01-04	Different construct 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 982–1266（285 aa） Chain C 982–1266（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 25% PEG MME 5000	Resolution 3.35 Å R-free 0.262
8XPT The Crystal Structure of EHMT1 from Biortus. Deposited 2024-01-04	Different construct 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 982–1266（285 aa） Chain D 982–1266（285 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ZN ZINC ION × 8 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Li2SO4, 0.1M Tris-HCl pH8.5, 25% PEG MME 5000	Resolution 3.35 Å R-free 0.262
9YKR Crystal structure of the GLP (EHMT1) SET domain in complex with SAM and TNG917 Deposited 2025-10-07	Different construct 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 1006–1266（261 aa） Fragment：catalytic SET domain (UNP residues 1006-1266) Chain B 1006–1266（261 aa） Fragment：catalytic SET domain (UNP residues 1006-1266)	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 PEG DI(HYDROXYETHYL)ETHER × 4 SO4 SULFATE ION × 16 EDO 1,2-ETHANEDIOL × 21	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；298 K；30% PEG3350, 200 mM lithium sulfate, 100 mM Bis-Tris, pH 5.5	Resolution 1.38 Å R-free 0.154

21 other PDB entries and 43 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EHMT1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–285； UniProt 982–1266 Author chain B； PDBConstruct 1–285； UniProt 982–1266

DNA (cytosine-5)-methyltransferase 3A

OrganismNot specified

UniProt O88508

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 P； UniProt 39–50	Fragment：unp residues 39-50 Non-standard monomer：Yes (specific site not provided by mmCIF)	Histone-lysine N-methyltransferase EHMT1 × 1 （Q9H9B1） ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.227
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Q； UniProt 39–50	Fragment：unp residues 39-50 Non-standard monomer：Yes (specific site not provided by mmCIF)	Histone-lysine N-methyltransferase EHMT1 × 1 （Q9H9B1） ZN ZINC ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.227
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain P； UniProt 39–50 Chain Q； UniProt 39–50	Fragment：unp residues 39-50 Non-standard monomer：Yes (specific site not provided by mmCIF)	Histone-lysine N-methyltransferase EHMT1 × 2 （Q9H9B1） ZN ZINC ION × 8 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.33 Å R-free 0.227

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3SWC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 39–50（12 aa） Fragment：unp residues 39-50	Not recorded	ZN ZINC ION × 4 SFG SINEFUNGIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.05 Å R-free 0.248
3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 39–50（12 aa） Fragment：unp residues 39-50	Not recorded	ZN ZINC ION × 4 SFG SINEFUNGIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.05 Å R-free 0.248
3SW9 GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me0 peptide Deposited 2011-07-13	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 39–50（12 aa） Fragment：unp residues 39-50 Chain Q 39–50（12 aa） Fragment：unp residues 39-50	Not recorded	ZN ZINC ION × 8 SFG SINEFUNGIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；0.1 M Hepes, 16% polyethylene glycol 4000 and 8% isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.05 Å R-free 0.248

1 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DNM3A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–12； UniProt 39–50 Author chain Q； PDBConstruct 1–12； UniProt 39–50

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	3swc
Deposition date deposition_date	2011-07-13
Structure title title	GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide
Keywords keywords	epigenetics, non-histone lysine methylation, SET domain, protein lysine methyltransferase, TRANSFERASE; TRANSFERASE
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	26.23 Å
Radius of gyration Rg (electron density) rg_electron	25.32 Å
Forward intensity I(0) i0	73378500.00
Molecular weight molecular_weight	62650.0 kDa
Excluded volume excluded_volume	76342 Å³
Envelope volume envelope_volume	91785 Å³
Hydration-shell volume shell_volume	30372 Å³
Envelope diameter envelope_diameter	88.4 Å
Shell Rg shell_rg	32.56 Å
Envelope Rg envelope_rg	25.17 Å
Shape Rg shape_rg	25.32 Å
Total Rg total_rg	26.02 Å
Total atoms total_atoms	4350
Residues n_residues	537
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	85.0 Å
Rg (real space) rg_real	26.21 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	7.3380e+07
I(0) uncertainty (real space) i0_real_error	9.8260e+05
Rg (reciprocal space) rg_reciprocal	26.22 Å
I(0) (reciprocal space) i0_reciprocal	73380000.0000
Solution quality estimate total_estimate	0.8884
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.357
Kurtosis Kurtosis kurtosis	-0.228
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6020000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.924

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase EHMT1
Molecular weight formula_weight	32830.2 kDa
EC 编号 ec_number	2.1.1.-, 2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4528

NSQVWSALQMSKALQDSAPDRPSPVERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS

来源 Source

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

Entity 2 Entity 2 polymer

Description description	DNA (cytosine-5)-methyltransferase 3A
Molecular weight formula_weight	1286.5 kDa
EC 编号 ec_number	2.1.1.37
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q

SATARKVGRPGR

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3swcA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

Domain ID domain_id	3swcB00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	270 — Beta-clip-like
Homologous superfamily homologous superfamily	10 — SET domain

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8. Citations (1)

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Unit-cell length a length_a	80.090 Å
Unit-cell length b length_b	90.220 Å
Unit-cell length c length_c	95.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.332 Å
Low-resolution limit resolution_low	40.780 Å
R factor r_factor	0.1897
R_work r_work	0.1869
R_free r_free	0.2274

fit	/app/data/saxs_computation/sw/3swc/3swc.fit
pddf	/app/data/pr_computation/sw/3swc/3swc.pr.out
profile	/app/data/saxs_computation/sw/3swc/3swc.dat

GLP (G9a-like protein) SET domain in complex with Dnmt3aK44me2 peptide

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

Histone-lysine N-methyltransferase EHMT1

State in the Current Structure

Other States of the Same Protein in the Database

DNA (cytosine-5)-methyltransferase 3A

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)