5v21

Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM

Method: X-RAY DIFFRACTION D_max: 68.9 Å Quality: GOOD

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

Histone-lysine N-methyltransferase SETD2

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 1435–1711	Fragment：SET domain (UNP residues 1435-1711)	Histone H3K36M peptide × 1 ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M KSCN, 24% (v/v) PEG 2000 MME	Resolution 2.42 Å R-free 0.269

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 5V21	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2A7O Solution Structure of the hSet2/HYPB SRI domain Deposited 2005-07-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1954–2061（108 aa） Fragment：Set2 Rpb1-interacting (SRI) domain, HSET2/HYBP SRI domain, residues 1954-2061	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient NMR sample composition U-15N (random labeling) HYPB, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition U-95% 13C, U-98% 15N labeled HYPB, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition Residue selective labeling with 15N-lysine HYPB, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition U-95% 13C, U-98% 15N HYPB, 100% D2O \| 100% D2O NMR sample composition Unlabeled HYPB,100% D2O \| 100% D2O NMR sample composition 10% 13C (fractional labeling) HYPB,100% D2O \| 100% D2O	Resolution not provided
2MDC Solution structure of the WW domain of HYPB Deposited 2013-09-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2385–2430（46 aa） Fragment：UNP residues 2385- 2430	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition 500 mM [U-99% 13C; U-99% 15N] H2O-1, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MDI Solution structure of the PP2WW mutant (KPP2WW) of HYPB Deposited 2013-09-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2377–2430（54 aa） Fragment：UNP residues 2377-2430	Mutation：K11A, P12A, K13A	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition 500 uM [U-99% 13C; U-99% 15N] KPP2WW-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 5%(w/v) sodium azide-4, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2MDJ Solution structure of WW domain with polyproline stretch (PP2WW) of HYPB Deposited 2013-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2377–2430（54 aa） Fragment：UNP residues 2377-2430	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient NMR sample composition 500uM [U-99% 13C; U-99% 15N] PP2WW-1, 20mM sodium phosphate-2, 50mM sodium chloride-3, 0.05%(w/v) sodium azide-4, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
4FMU Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF Deposited 2012-06-18	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 1434–1711（278 aa）	Not recorded	ZN ZINC ION × 3 0UM (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid × 1 UNX UNKNOWN LIGAND × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG4000, 10% isoprpanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.235
4H12 The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine Deposited 2012-09-10	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 1434–1711（278 aa） Fragment：methyltransferase domain (UNP residues 1434-1711)	Not recorded	ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；1 uL protein (1:10 molar ratio of SETD2:AdoMet) + 1 uL reservoir solution (30% PEG2000 MME, 0.1 M potassium thiocyanate), VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.06 Å R-free 0.249
5JJY Crystal structure of SETD2 bound to histone H3.3 K36M peptide Deposited 2016-04-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1434–1711（278 aa） Fragment：catalytic domain, UNP residues 1434-1711	Not recorded	ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350	Resolution 2.05 Å R-free 0.213
5JLB Crystal structure of SETD2 bound to histone H3.3 K36I peptide Deposited 2016-04-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1434–1711（278 aa） Fragment：catalytic domain, UNP residues 1434-1711	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 3 GOL GLYCEROL × 2 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350	Resolution 1.50 Å R-free 0.190
5JLE Crystal structure of SETD2 bound to SAH Deposited 2016-04-27	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 1434–1711（278 aa） Fragment：catalytic domain, UNP residues 1434-1711	Not recorded	ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M KSCN, 30% PEG2000mme	Resolution 2.40 Å R-free 0.250
5LSS Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05	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 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76H [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-propyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M KSCN, 31.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7	Resolution 1.79 Å R-free 0.226
5LSX Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05	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 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 76O [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, pH 7.3, 0.1MKSCN, 25-30%MPEG2000	Resolution 2.90 Å R-free 0.280
5LSY Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05	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 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76M [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(2-methylpropyl)azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000	Resolution 1.62 Å R-free 0.215
5LSZ Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05	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 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 SCN THIOCYANATE ION × 2 76K [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(3-oxidanylpropyl)azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes pH7.3, 0.1MKSCN, 25-30%MPEG2000	Resolution 1.62 Å R-free 0.201
5LT6 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06	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 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76J [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000.	Resolution 2.05 Å R-free 0.231
5LT6 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06	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 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76J [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000.	Resolution 2.05 Å R-free 0.231
5LT7 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06	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 1433–1711（279 aa）	Not recorded	ZN ZINC ION × 3 SCN THIOCYANATE ION × 2 76L [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-[(2~{R})-2-oxidanylpropyl]azanium × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000	Resolution 1.51 Å R-free 0.192
5LT8 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06	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 1433–1711（279 aa）	Not recorded	ZN ZINC ION × 3 SFG SINEFUNGIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES, PH7.3, 0.1MKSCN, 25-30%MPEG2000	Resolution 1.57 Å R-free 0.216
5V22 Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAH Deposited 2017-03-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1435–1711（277 aa） Fragment：SET domain (UNP residues 1435-1711)	Not recorded	ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M KSCN, 24% (v/v) PEG 2000 MME	Resolution 2.40 Å R-free 0.257
6J9J crystal structure of SESTD2 in complex with H3.3S31phK36M peptide Deposited 2019-01-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1447–1703（257 aa）	Not recorded	ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M potassium thiocyanate, 0.1M Bis-Tris propane,20% PEG 3350	Resolution 1.78 Å R-free 0.206
6VDB SETD2 in complex with a H3-variant super-substrate peptide Deposited 2019-12-24	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1433–1711（279 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 20 ZN ZINC ION × 3 SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M KSCN, 0.1 M Tris-HCl pH 8.5, and 26% PEG 3350	Resolution 2.30 Å R-free 0.263
7EA8 Human SETD2 bound to a nucleosome containing oncohistone mutations Deposited 2021-03-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain L 1452–1696（245 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7EVR Crystal structure of hnRNP L RRM2 in complex with SETD2 Deposited 2021-05-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2167–2192（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Potassium/Sodium phosphate, pH 7.5	Resolution 1.80 Å R-free 0.198
7EVR Crystal structure of hnRNP L RRM2 in complex with SETD2 Deposited 2021-05-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2167–2192（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Potassium/Sodium phosphate, pH 7.5	Resolution 1.80 Å R-free 0.198
7EVS Crystal structure of hnRNP LL RRM2 in complex with SETD2 Deposited 2021-05-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2180–2192（13 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3M Ammonium Sulfate, 20% PEG 4000	Resolution 1.60 Å R-free 0.204
7EVS Crystal structure of hnRNP LL RRM2 in complex with SETD2 Deposited 2021-05-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2180–2192（13 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.3M Ammonium Sulfate, 20% PEG 4000	Resolution 1.60 Å R-free 0.204
7LZB Crystal Structure of SETD2 bound to Compound 2 Deposited 2021-03-09	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 1434–1711（278 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YJ1 N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide × 1 BME BETA-MERCAPTOETHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1M Tris pH 7.8, 25% w/v PEG 2000 MME	Resolution 2.28 Å R-free 0.264
7LZD Crystal Structure of SETD2 bound to Compound 35 Deposited 2021-03-09	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 1434–1711（278 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YHY N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 9 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M HEPES pH 7.5, 24% w/v PEG 2000 MME	Resolution 1.80 Å R-free 0.218
7LZF Crystal Structure of SETD2 bound to Compound 57 Deposited 2021-03-09	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 1434–1711（278 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YHV 4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl)(methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME	Resolution 2.47 Å R-free 0.263
7TY2 Crystal Structure of SETD2 Bound to an Indole-based Inhibitor Deposited 2022-02-11	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 1434–1711（278 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 KS6 N-[(1R,3S)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M HEPES 7.5, 18% w/v PEG 2000 MME	Resolution 2.44 Å R-free 0.270
7TY3 Crystal Structure of SETD2 Bound to an Indole-based Inhibitor Deposited 2022-02-11	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 1434–1711（278 aa）	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 KRF N-[(1R,3R)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME	Resolution 2.30 Å R-free 0.270
8Q5P Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from human tyrosine kinase ACK1 Deposited 2023-08-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1433–1711（279 aa） Fragment：UNP residues 1433-1711	Not recorded	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；0.1M TRIS pH 8.5, 16%w/v PEG 10000	Resolution 1.81 Å R-free 0.246
8RZU Structure of human SETD2 L1609P mutant in complex with SAM and H3K36M peptide Deposited 2024-02-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1433–1711（279 aa）	Mutation：L1609P	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；32% w/v PEG 4K, 100mM Tris, 800mM LiCl, pH 8.5	Resolution 2.19 Å R-free 0.264
9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain l 1435–2564（1130 aa）	Not recorded	ZN ZINC ION × 12 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain l 1435–2564（1130 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain l 1452–2040（589 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain l 1435–2564（1130 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9G4A Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide Deposited 2024-07-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1433–1711（279 aa）	Mutation：T1663M	ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；32% w/v PEG 4K, 100mM Tris, 800mM LiCl	Resolution 1.65 Å R-free 0.241
9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain O 1435–2564（1130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.84 Å
9HGG SETD2 peptide bound to SPOP MATH domain Deposited 2024-11-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1363–1379（17 aa）	Not recorded	MG MAGNESIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5	Resolution 1.90 Å R-free 0.256
9RTN State 2 MAP 2 SPT6 with SETD2 Deposited 2025-07-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain O 1435–2564（1130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.82 Å
9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric	Chain O 1435–2564（1130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.66 Å
9RZD State 3 MAP 2 SPT6 with SETD2 Deposited 2025-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain O 1435–2564（1130 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.69 Å
9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric	Chain O 1435–2564（1130 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.53 Å
9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric	Chain O 1435–2564（1130 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.72 Å
9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric	Chain O 1435–2564（1130 aa）	Not recorded	ZN ZINC ION × 9 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 Å

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

View Construct and Data Evidence

UniProt name	SETD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–297； UniProt 1435–1711

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	5v21
Deposition date deposition_date	2017-03-02
Structure title title	Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM
Keywords keywords	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	20.20 Å
Radius of gyration Rg (electron density) rg_electron	19.16 Å
Forward intensity I(0) i0	18516700.00
Molecular weight molecular_weight	30388.0 kDa
Excluded volume excluded_volume	37105 Å³
Envelope volume envelope_volume	44037 Å³
Hydration-shell volume shell_volume	19471 Å³
Envelope diameter envelope_diameter	70.2 Å
Shell Rg shell_rg	25.46 Å
Envelope Rg envelope_rg	19.61 Å
Shape Rg shape_rg	19.11 Å
Total Rg total_rg	20.16 Å
Total atoms total_atoms	2111
Residues n_residues	260
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	68.9 Å
Rg (real space) rg_real	20.16 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.8520e+07
I(0) uncertainty (real space) i0_real_error	2.3500e+05
Rg (reciprocal space) rg_reciprocal	20.17 Å
I(0) (reciprocal space) i0_reciprocal	18520000.0000
Solution quality estimate total_estimate	0.8765
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.296
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.3950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3020000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.811; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.962

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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 SETD2
Molecular weight formula_weight	34368.2 kDa
EC 编号 ec_number	2.1.1.43
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	2147

MHHHHHHSSGRENLYFQGHMETSVPPGSALVGPSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGKMKKERSRK

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	Histone H3K36M peptide
Molecular weight formula_weight	1641.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

APATGGVMKPHRYRP

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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8. Citations (1)

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Unit-cell length a length_a	58.493 Å
Unit-cell length b length_b	76.316 Å
Unit-cell length c length_c	77.179 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	4

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

Resolution resolution	2.415 Å
Low-resolution limit resolution_low	29.528 Å
R factor r_factor	0.2073
R_work r_work	0.2040
R_free r_free	0.2693

fit	/app/data/saxs_computation/v2/5v21/5v21.fit
pddf	/app/data/pr_computation/v2/5v21/5v21.pr.out
profile	/app/data/saxs_computation/v2/5v21/5v21.dat

Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM

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

Histone-lysine N-methyltransferase SETD2

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)