3m59

SET7/9 Y245A in complex with TAF10-K189me2 peptide and AdoHcy

Method: X-RAY DIFFRACTION D_max: 68.5 Å Quality: GOOD

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

Histone-lysine N-methyltransferase SETD7

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 110–366	Fragment：UNP residues 110-366 Mutation：Y245A	TAF10-K189me2 Peptide × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 CO COBALT (II) ION × 3 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；1.9 M Ammonium Sulfate, 0.1 M Bis-Tris pH 6.4, 0.005 M CoCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.206

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 3M59	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1H3I Crystal structure of the Histone Methyltransferase SET7/9 Deposited 2002-09-04	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 106–398（293 aa） Fragment：N-DOMAIN, SET-DOMAIN, RESIDUES 52-344	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.10 Å R-free 0.255
1H3I Crystal structure of the Histone Methyltransferase SET7/9 Deposited 2002-09-04	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 106–398（293 aa） Fragment：N-DOMAIN, SET-DOMAIN, RESIDUES 52-344	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.10 Å R-free 0.255
1MT6 Structure of histone H3 K4-specific methyltransferase SET7/9 with AdoHcy Deposited 2002-09-20	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 58–337（280 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；283 K；PEG 4000, sodium citrate, Isopropanol, DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.20 Å R-free 0.263
1MUF Structure of histone H3 K4-specific methyltransferase SET7/9 Deposited 2002-09-23	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 81–337（257 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；PEG 3000, CaCl2, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.26 Å R-free 0.249
1N6A Structure of SET7/9 Deposited 2002-11-09	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 108–366（259 aa） Fragment：residues 108-366	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG6000, Tris-HCl, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.217
1N6C Structure of SET7/9 Deposited 2002-11-09	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 70–366（297 aa） Fragment：residues 70-366	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；291 K；Ammonium sulfate, Lithium sulfate, Sodium citrate, DTT, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.30 Å R-free 0.243
1O9S Crystal structure of a ternary complex of the human histone methyltransferase SET7/9 Deposited 2002-12-18	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 108–366（259 aa） Fragment：N-DOMAIN, SET-DOMAIN, RESIDUES 108-366	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.80	Resolution 1.75 Å R-free 0.222
1O9S Crystal structure of a ternary complex of the human histone methyltransferase SET7/9 Deposited 2002-12-18	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 108–366（259 aa） Fragment：N-DOMAIN, SET-DOMAIN, RESIDUES 108-366	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；pH 7.80	Resolution 1.75 Å R-free 0.222
1XQH Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH Deposited 2004-10-12	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 108–366（259 aa） Fragment：N-domain, SET-domain	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；291 K；PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K	Resolution 1.75 Å R-free 0.223
1XQH Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH Deposited 2004-10-12	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 E 108–366（259 aa） Fragment：N-domain, SET-domain	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.8；291 K；PEG3350, Tris-HCL, pH 7.8, VAPOR DIFFUSION, temperature 291K	Resolution 1.75 Å R-free 0.223
2F69 Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide Deposited 2005-11-28	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 110–366（257 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.89-2.04 M (NH4)2SO4, 0.1 M Bis TRIS pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.30 Å R-free 0.174
3CBM SET7/9-ER-AdoMet complex Deposited 2008-02-22	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 111–366（256 aa） Fragment：UNP residues 111-366	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 BME BETA-MERCAPTOETHANOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION	Resolution 1.69 Å R-free 0.229
3CBO SET7/9-ER-AdoHcy complex Deposited 2008-02-22	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 111–366（256 aa） Fragment：UNP residues 111-366	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 BME BETA-MERCAPTOETHANOL × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION	Resolution 1.65 Å R-free 0.231
3CBO SET7/9-ER-AdoHcy complex Deposited 2008-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 111–366（256 aa） Fragment：UNP residues 111-366	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 BME BETA-MERCAPTOETHANOL × 6 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION	Resolution 1.65 Å R-free 0.231
3CBP Set7/9-ER-Sinefungin complex Deposited 2008-02-22	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 111–366（256 aa） Fragment：UNP residues 111-366	Not recorded	SFG SINEFUNGIN × 1 BME BETA-MERCAPTOETHANOL × 3 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；40-42.5% PEG3350, 100 mM Tris, pH 8.0, VAPOR DIFFUSION, pH 8.00	Resolution 1.42 Å R-free 0.243
3M53 SET7/9 in complex with TAF10 peptide and AdoHcy Deposited 2010-03-12	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 110–366（257 aa） Fragment：UNP residues 110-366	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；1.8 M Sodium Citrate, 0.1 M Imidazole pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.85 Å R-free 0.224
3M54 SET7/9 Y305F in complex with TAF10 peptide and AdoHcy Deposited 2010-03-12	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 110–366（257 aa） Fragment：UNP residues 110-366	Mutation：Y305F	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；1.2 M Sodium Citrate, 0.1 M Imidazole pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.219
3M55 SET7/9 Y305F in complex with TAF10-K189me1 peptide and AdoHcy Deposited 2010-03-12	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 110–366（257 aa） Fragment：UNP residues 110-366	Mutation：Y305F	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；0.95 M Sodium Citrate, 0.1 M Imidazole pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.55 Å R-free 0.217
3M56 SET7/9 Y305F in complex with TAF10-K189me2 peptide and AdoHcy Deposited 2010-03-12	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 110–366（257 aa） Fragment：UNP residues 110-366	Mutation：Y305F	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.1 M Sodium Citrate, 0.1 M Imidazole pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.65 Å R-free 0.221
3M57 SET7/9 Y245A in complex with TAF10 peptide and AdoHcy Deposited 2010-03-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–366（257 aa） Fragment：UNP residues 110-366	Mutation：Y245A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.9 M Sodium Citrate, 0.1 M Imidazole pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.221
3M58 SET7/9 Y245A in complex with TAF10-K189me1 peptide and AdoHcy Deposited 2010-03-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–366（257 aa） Fragment：UNP residues 110-366	Mutation：Y245A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；1.9 M Ammonium Sulfate, 0.1 M Bis-Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.40 Å R-free 0.198
3M5A SET7/9 Y245A in complex with TAF10-K189me3 peptide and AdoHcy Deposited 2010-03-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 110–366（257 aa） Fragment：UNP residues 110-366	Mutation：Y245A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 CO COBALT (II) ION × 7 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；293 K；1.7 M Ammonium Sulfate, 0.1 M Bis-Tris pH 6.6, 0.0025 M CoCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.75 Å R-free 0.210
3OS5 SET7/9-Dnmt1 K142me1 complex Deposited 2010-09-08	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 111–366（256 aa）	Not recorded	BME BETA-MERCAPTOETHANOL × 1 EDO 1,2-ETHANEDIOL × 5 UNL UNKNOWN LIGAND × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；289 K；40% PEG3350, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.69 Å R-free 0.238
3VUZ Crystal structure of histone methyltransferase SET7/9 in complex with AAM-1 Deposited 2012-07-10	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 111–366（256 aa） Fragment：UNP residues 111-366	Not recorded	K15 5'-{[(3S)-3-amino-3-carboxypropyl](hexyl)amino}-5'-deoxyadenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris-HCl pH8.3-8.5, 28-30% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.50 Å R-free 0.247
3VV0 Crystal structure of histone methyltransferase SET7/9 in complex with DAAM-3 Deposited 2012-07-10	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 111–366（256 aa） Fragment：residues 111-366	Not recorded	KH3 5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]amino}-5'-deoxyadenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M Tris-HCl pH8.3-8.5, 28-30% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.232
4E47 SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine Deposited 2012-03-12	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 109–366（258 aa） Fragment：SET domain (UNP residues 109-366)	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 0N6 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 BME BETA-MERCAPTOETHANOL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；40% PEG3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.201
4E47 SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine Deposited 2012-03-12	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 109–366（258 aa） Fragment：SET domain (UNP residues 109-366)	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 0N6 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；40% PEG3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.201
4E47 SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine Deposited 2012-03-12	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 109–366（258 aa） Fragment：SET domain (UNP residues 109-366)	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 0N6 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；40% PEG3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.201
4E47 SET7/9 in complex with inhibitor (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6- sulfonamide and S-adenosylmethionine Deposited 2012-03-12	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 109–366（258 aa） Fragment：SET domain (UNP residues 109-366)	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 0N6 (R)-(3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl)-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；40% PEG3350, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.201
4J7F SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy Deposited 2013-02-13	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 110–366（257 aa）	Mutation：Y335pAF Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.59 Å R-free 0.215
4J7F SET7/9Y335pAF in complex with TAF10 peptide and AdoHcy Deposited 2013-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 110–366（257 aa）	Mutation：Y335pAF Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.59 Å R-free 0.215
4J7I SET7/9Y335F in complex with TAF10 peptide and AdoHcy Deposited 2013-02-13	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 110–366（257 aa）	Mutation：Y335F	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.56 Å R-free 0.257
4J7I SET7/9Y335F in complex with TAF10 peptide and AdoHcy Deposited 2013-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 110–366（257 aa）	Mutation：Y335F	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.56 Å R-free 0.257
4J83 SET7/9 in complex with TAF10K189A peptide and AdoMet Deposited 2013-02-14	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 110–366（257 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.211
4J83 SET7/9 in complex with TAF10K189A peptide and AdoMet Deposited 2013-02-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 110–366（257 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.70 Å R-free 0.211
4J8O SET7/9 in complex with TAF10K189A peptide and AdoHcy Deposited 2013-02-14	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 110–366（257 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；sodium citrate, imidazole, nickel chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.63 Å R-free 0.228
4JDS SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine Deposited 2013-02-25	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 109–366（258 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 2 1L4 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 2 UNX UNKNOWN LIGAND × 28	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.70 Å R-free 0.223
4JDS SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine Deposited 2013-02-25	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 109–366（258 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 1L4 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.70 Å R-free 0.223
4JDS SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine Deposited 2013-02-25	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 109–366（258 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 1L4 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.70 Å R-free 0.223
4JDS SETD7 in complex with inhibitor PF-5426 and S-adenosyl-methionine Deposited 2013-02-25	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 109–366（258 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 1L4 N-[(2R)-3-(3-cyanophenyl)-1-oxo-1-(pyrrolidin-1-yl)propan-2-yl]-8-fluoro-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；25% PEG 3350, 0.1 M Ammonium Sulfate, 0.1 M BisTris pH6.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.70 Å R-free 0.223
4JLG SETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine Deposited 2013-03-12	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 109–366（258 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 1L8 8-fluoro-N-{(2R)-1-oxo-1-(pyrrolidin-1-yl)-3-[3-(trifluoromethyl)phenyl]propan-2-yl}-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNX UNKNOWN LIGAND × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；23% PEG 3500, 0.2 M Lithium Sulfate, 0.1 M BisTris pH 6.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.90 Å R-free 0.237
4JLG SETD7 in complex with inhibitor (R)-PFI-2 and S-adenosyl-methionine Deposited 2013-03-12	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 109–366（258 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 1L8 8-fluoro-N-{(2R)-1-oxo-1-(pyrrolidin-1-yl)-3-[3-(trifluoromethyl)phenyl]propan-2-yl}-1,2,3,4-tetrahydroisoquinoline-6-sulfonamide × 1 UNX UNKNOWN LIGAND × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；23% PEG 3500, 0.2 M Lithium Sulfate, 0.1 M BisTris pH 6.5, vapor diffusion hanging drop, temperature 291K	Resolution 1.90 Å R-free 0.237
5AYF Crystal structure of SET7/9 in complex with cyproheptadine Deposited 2015-08-20	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 111–366（256 aa） Fragment：UNP residues 111-366	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 C7H 4-(dibenzo[1,2-a:2',1'-d][7]annulen-11-ylidene)-1-methyl-piperidine × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M Tris-HCl pH 8.5, 31% PEG 6000	Resolution 2.00 Å R-free 0.258
5EG2 SET7/9 N265A in complex with AdoHcy and TAF10 peptide Deposited 2015-10-26	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 110–366（257 aa）	Mutation：N265A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；1:1 ratio of protein solution to crystallization solution. Protein solution: 4.0-8.0 mg/mL protein, 2.5 mM AdoMet, 2.0 mM TAF10 peptide, and 2.0 mM TCEP Crystallant solution: 0.99 - 1.02 M sodium citrate, 12 - 22 mM nickel (II) chloride, and 100 mM imidazole pH 8.4	Resolution 1.55 Å R-free 0.171
5YLT Crystal structure of SET7/9 in complex with a cyproheptadine derivative Deposited 2017-10-19	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 111–366（256 aa）	Not recorded	SFG SINEFUNGIN × 1 C7N 2-(1-methylpiperidin-4-ylidene)tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3(8),4,6,9,12,14-heptaen-6-ol × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M TRIS-HCL PH 8.5, 34% PEG 6000	Resolution 1.69 Å R-free 0.200

31 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SETD7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–261； UniProt 110–366

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	3m59
Deposition date deposition_date	2010-03-12
Structure title title	SET7/9 Y245A in complex with TAF10-K189me2 peptide and AdoHcy
Keywords keywords	;TERNARY COMPLEX, SET DOMAIN, METHYLTRANSFERASE, S-ADENOSYL-L-HOMOCYSTEINE, TAF10 PEPTIDE, N-DIMETHYLLYSINE, Chromatin regulator, Chromosomal protein, Nucleus, S-adenosyl-L-methionine, Transcription, Transcription regulation, 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	20.16 Å
Radius of gyration Rg (electron density) rg_electron	19.23 Å
Forward intensity I(0) i0	15333800.00
Molecular weight molecular_weight	28673.0 kDa
Excluded volume excluded_volume	35458 Å³
Envelope volume envelope_volume	40907 Å³
Hydration-shell volume shell_volume	18301 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	25.22 Å
Envelope Rg envelope_rg	19.64 Å
Shape Rg shape_rg	19.20 Å
Total Rg total_rg	20.15 Å
Total atoms total_atoms	2008
Residues n_residues	252
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	68.5 Å
Rg (real space) rg_real	20.18 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.5330e+07
I(0) uncertainty (real space) i0_real_error	2.0250e+05
Rg (reciprocal space) rg_reciprocal	20.18 Å
I(0) (reciprocal space) i0_reciprocal	15330000.0000
Solution quality estimate total_estimate	0.8693
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.187
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4008000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase SETD7
Molecular weight formula_weight	28951.2 kDa
EC 编号 ec_number	2.1.1.43
Mutation mutation	Y245A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2296

GAMGYKDNIRHGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFANGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQK

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	TAF10-K189me2 Peptide
Molecular weight formula_weight	1282.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XSKSKDRKYTL

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	237

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3m59A01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	110 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain
Homologous superfamily homologous superfamily	10 — Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain

Domain ID domain_id	3m59A02
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	83.497 Å
Unit-cell length b length_b	83.497 Å
Unit-cell length c length_c	95.718 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	6

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	36.160 Å
R factor r_factor	0.1880
R_work r_work	0.1870
R_free r_free	0.2060

fit	/app/data/saxs_computation/m5/3m59/3m59.fit
pddf	/app/data/pr_computation/m5/3m59/3m59.pr.out
profile	/app/data/saxs_computation/m5/3m59/3m59.dat

SET7/9 Y245A in complex with TAF10-K189me2 peptide and AdoHcy

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

Histone-lysine N-methyltransferase SETD7

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 (6)

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 non-polymer

Entity 6 Entity 6 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)