9lhp

Crystal structure of human thymine DNA glycosylase TDG in complex with a covalent inhibitor (1S, 5R)-C-2711

Method: X-RAY DIFFRACTION D_max: 72.1 Å Quality: GOOD

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

G/T mismatch-specific thymine DNA glycosylase

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 113–326	Not recorded	Small ubiquitin-related modifier 1 × 1 （P63165） A1LYG (1~{S},2~{S})-2-[(2-methoxy-5-methyl-4-oxidanyl-phenyl)methyl]cyclopropane-1-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.1M TRIS, PH 8.5, 0.2M MAGNESIUM CHLORIDE	Resolution 2.14 Å R-free 0.243

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	G8JL98_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–214； UniProt 113–326

Small ubiquitin-related modifier 1

Homo sapiens

UniProt P63165

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–97	Not recorded	G/T mismatch-specific thymine DNA glycosylase × 1 （G8JL98） A1LYG (1~{S},2~{S})-2-[(2-methoxy-5-methyl-4-oxidanyl-phenyl)methyl]cyclopropane-1-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；25% PEG3350, 0.1M TRIS, PH 8.5, 0.2M MAGNESIUM CHLORIDE	Resolution 2.14 Å R-free 0.243

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9LHP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A5R STRUCTURE DETERMINATION OF THE SMALL UBIQUITIN-RELATED MODIFIER SUMO-1, NMR, 10 STRUCTURES Deposited 1998-02-18	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 1–101（101 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；300 K；Ionic strength (raw mmCIF value) 100 mM；Pressure STANDARD NMR sample composition H2O	Resolution not provided
1TGZ Structure of human Senp2 in complex with SUMO-1 Deposited 2004-05-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–97（80 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.276
1TGZ Structure of human Senp2 in complex with SUMO-1 Deposited 2004-05-31	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 18–97（80 aa）	Not recorded	SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.276
1WYW Crystal Structure of SUMO1-conjugated thymine DNA glycosylase Deposited 2005-02-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–97（97 aa）	Not recorded	CL CHLORIDE ION × 3 MG MAGNESIUM ION × 5 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；25% PEG3350, 0.1M Tris, 0.2M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.245
1Y8R SUMO E1 ACTIVATING ENZYME SAE1-SAE2-SUMO1-MG-ATP COMPLEX Deposited 2004-12-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–97（97 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；0.1M sodium acetate, 10mM ATP, 10-20% PEG 4000, 0.1-1.0M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.75 Å R-free 0.276
1Y8R SUMO E1 ACTIVATING ENZYME SAE1-SAE2-SUMO1-MG-ATP COMPLEX Deposited 2004-12-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–97（97 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；278 K；0.1M sodium acetate, 10mM ATP, 10-20% PEG 4000, 0.1-1.0M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.75 Å R-free 0.276
1Z5S Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2 Deposited 2005-03-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 18–97（80 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；18% PEG4000 (w/v), 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.01 Å R-free 0.290
2ASQ Solution Structure of SUMO-1 in Complex with a SUMO-binding Motif (SBM) Deposited 2005-08-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–97（97 aa） Fragment：Structured Region of SUMO-1 (residues 21-97)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR sample composition 1 mM 15N,13C-enriched PIASx-P peptide and unlabeled SUMO-1; 20mM phosphate buffer pH6.8; 92% H2O, 8% D2O, 17oC \| 92% H2O, 8% D2O NMR sample composition 1 mM 15N,13C-enriched SUMO-1 and unlabeled PIASx-P peptide; 20mM phosphate buffer pH6.8; 92% H2O, 8% D2O, 17oC \| 92% H2O, 8% D2O	Resolution not provided
2BF8 Crystal structure of SUMO modified ubiquitin conjugating enzyme E2- 25K Deposited 2004-12-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 21–97（77 aa） Fragment：RESIDUES 21-97	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；100 MM TRIS PH 8.5 200 MM MAGNESIUM CHLORIDE 17% PEG 4000 10 % GLYCEROL	Resolution 2.30 Å R-free 0.279
2G4D Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1 Deposited 2006-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–97（78 aa） Fragment：residues 20-97	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；289 K；0.1M CAPS, 40% PEG400, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.278
2G4D Crystal structure of human SENP1 mutant (C603S) in complex with SUMO-1 Deposited 2006-02-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–97（78 aa） Fragment：residues 20-97	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；289 K；0.1M CAPS, 40% PEG400, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.278
2IO2 Crystal structure of human Senp2 in complex with RanGAP1-SUMO-1 Deposited 2006-10-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric	Chain B 18–97（80 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；12% PEG 4000, 0.1M Lithium chloride, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.90 Å R-free 0.301
2IY0 SENP1 (mutant) SUMO1 RanGAP Deposited 2006-07-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–101（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.77 Å R-free 0.279
2IY1 SENP1 (mutant) full length SUMO1 Deposited 2006-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–101（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.46 Å R-free 0.281
2IY1 SENP1 (mutant) full length SUMO1 Deposited 2006-07-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–101（82 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.46 Å R-free 0.281
2KQS Phosphorylation of SUMO-interacting motif by CK2 enhances Daxx SUMO binding activity Deposited 2009-11-17	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–97（97 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.27-0.5mM [U-100% 15N] SUMO1-1, 0-1.7mM DAXX20-2, 10mM potassium phosphate-3, 100mM potassium chloride-4, 2mM DTT-5, 0.1mM EDTA-6, 0.001% sodium azide-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SUMO1-8, 2mM DAXX20-9, 10mM potassium phosphate-10, 100mM potassium chloride-11, 2mM DTT-12, 0.1mM EDTA-13, 0.001% sodium azide-14, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM SUMO1-15, 0.5mM [U-100% 13C; U-100% 15N] DAXX20-16, 10mM potassium phosphate-17, 100mM potassium chloride-18, 2mM DTT-19, 0.1mM EDTA-20, 0.001% sodium azide-21, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5mM [U-100% 13C; U-100% 15N] SUMO1-22, 0.5mM [U-100% 13C; U-100% 15N] DAXX20-23, 10mM potassium phosphate-24, 100mM potassium chloride-25, 2mM DTT-26, 0.1mM EDTA-27, 0.001% sodium azide-28, 0.0066 w/v Pf1 phage-29, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LAS Molecular Determinants of Paralogue-Specific SUMO-SIM Recognition Deposited 2011-03-20	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–101（101 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.5 mM [U-13C; U-15N; U-2H] SUMO1, 1.0 mM M-IR2 peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-15N]; perdeuterated SUMO1, 0.6 mM M-IR2 peptide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.6 mM [U-15N; U-2H] SUMO1, 0.4 mM M-IR2 peptide, 100% D2O \| 100% D2O	Resolution not provided
2MW5 Backbone fold of Human Small Ubiquitin like Modifier protein-1 (SUMO-1) based on Prot3D-NMR approach. Deposited 2014-10-28	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 1–97（97 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.8-1 mM [U-100% 13C; U-100% 15N] sodium phosphate-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N1A Docked structure between SUMO1 and ZZ-domain from CBP Deposited 2015-03-26	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–101（101 aa）	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 6；298 K；Pressure ambient NMR sample composition 20 mM MES, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 20 mM MES, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2N1V Solution structure of human SUMO1 Deposited 2015-04-24	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 1–97（97 aa） Fragment：UNP residues 1-97	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Pressure ambient NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] SUMO1-1, 10 mM potassium phosphate-2, 100 mM potassium chloride-3, 2 mM DTT-4, 0.1 mM EDTA-5, 0.001 % sodium azide-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 15N] SUMO1-7, 10 mM potassium phosphate-8, 100 mM potassium chloride-9, 2 mM DTT-10, 0.1 mM EDTA-11, 0.001 % sodium azide-12, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM [U-100% 15N] SUMO1-13, 10 mM potassium phosphate-14, 100 mM potassium chloride-15, 2 mM DTT-16, 0.1 mM EDTA-17, 0.001 % sodium azide-18, 10 w/v Pf1 phage-19, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5-1 mM SUMO1-20, 10 mM potassium phosphate-21, 100 mM potassium chloride-22, 2 mM DTT-23, 0.1 mM EDTA-24, 0.001 % sodium azide-25, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2PE6 Non-covalent complex between human SUMO-1 and human Ubc9 Deposited 2007-04-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–97（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；291 K；100 mM Tris-HCl, pH 8.5, 25% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.50	Resolution 2.40 Å R-free 0.250
2UYZ Non-covalent complex between Ubc9 and SUMO1 Deposited 2007-04-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–97（78 aa） Fragment：RESIDUES 20-97	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；16.5 % (W/V) PEG3350 100 MM BISTRIS PH 5.5 15 % (W/V) GLYCEROL	Resolution 1.40 Å R-free 0.178
2VRR Structure of SUMO modified Ubc9 Deposited 2008-04-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–97（78 aa） Fragment：RESIDUES 20-97	Not recorded	FMT FORMIC ACID × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；24% (W/V) PEG3350, 200 MM SODIUM FORMATE, 100 MM BIS-TRIS PROPANE PH6.5	Resolution 2.22 Å R-free 0.256
3KYC Human SUMO E1 complex with a SUMO1-AMP mimic Deposited 2009-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–97（97 aa） Fragment：UNP residues 1-97	Mutation：T95C	ZN ZINC ION × 1 JZU 5'-deoxy-5'-(sulfamoylamino)adenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；291 K；0.1 MES, 24% PEG 3350, 1.3 M AMMONIUM ACETATE, 10 mM ATP, 10 mM MgCl2, 10 mM TCEP, 2.5% PEG 400, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.45 Å R-free 0.250
3KYD Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic Deposited 2009-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–96（96 aa） Fragment：UNP residues 1-96	Mutation：T95C	EDO 1,2-ETHANEDIOL × 3 ZN ZINC ION × 1 VMX 5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；279 K；22% PEG 2000 MME, 0.2 M di-ammonium tartrate, 3% EtGly, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.61 Å R-free 0.284
3RZW Crystal Structure of the Monobody ySMB-9 bound to human SUMO1 Deposited 2011-05-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–97（97 aa）	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；292 K；24% PEG-8000, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, temperature 292K	Resolution 2.15 Å R-free 0.237
3RZW Crystal Structure of the Monobody ySMB-9 bound to human SUMO1 Deposited 2011-05-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–97（97 aa）	Mutation：C52A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；292 K；24% PEG-8000, 0.1M Imidazole, pH 8.0, VAPOR DIFFUSION, temperature 292K	Resolution 2.15 Å R-free 0.237
3UIP Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 18–97（80 aa） Fragment：UNP residues 18-97	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；22% PEG4000, 100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K	Resolution 2.29 Å R-free 0.232
4WJN Crystal structure of SUMO1 in complex with phosphorylated PML Deposited 2014-10-01	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 17–97（81 aa） Fragment：SUMO1, unp residues 17-97	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM sodium cacodylate, 16% PEG3350, 10mM calcium chloride	Resolution 1.50 Å R-free 0.192
4WJO Crystal Structure of SUMO1 in complex with PML Deposited 2014-10-01	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 17–97（81 aa） Fragment：SUMO1, unp residues 17-97	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM sodium cacodylate pH6.5, 16% PEG3350, 10mM calcium chloride	Resolution 1.46 Å R-free 0.184
4WJP Crystal Structure of SUMO1 in complex with phosphorylated Daxx Deposited 2014-10-01	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 17–97（81 aa） Fragment：unp residues 17-97	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM sodium cacodylate, 26% PEG3350, 10mM CaCl2	Resolution 1.70 Å R-free 0.195
4WJP Crystal Structure of SUMO1 in complex with phosphorylated Daxx Deposited 2014-10-01	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 C 17–97（81 aa） Fragment：unp residues 17-97	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100mM sodium cacodylate, 26% PEG3350, 10mM CaCl2	Resolution 1.70 Å R-free 0.195
4WJQ Crystal Structure of SUMO1 in complex with Daxx Deposited 2014-10-01	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 17–97（81 aa） Fragment：unp residues 17-97	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium cacodylate, 26% PEG3350, 10 mM calcium chloride	Resolution 1.35 Å R-free 0.181
4WJQ Crystal Structure of SUMO1 in complex with Daxx Deposited 2014-10-01	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 C 17–97（81 aa） Fragment：unp residues 17-97	Mutation：C52A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM sodium cacodylate, 26% PEG3350, 10 mM calcium chloride	Resolution 1.35 Å R-free 0.181
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	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 B 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain T 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 11 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain V 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 12 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	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 D 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain N 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5AEK Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W Deposited 2014-12-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 20–97（78 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 291 K；2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K	Resolution 3.00 Å R-free 0.326
5B7A SOLUTION STRUCTURE OF LYS37 ACETYLATED HUMAN SUMO1 Deposited 2016-06-05	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 1–97（97 aa） Fragment：UNP residues 1-97	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure AMBIENT NMR sample composition 1 mM [U-100% 13C; U-100% 15N] SUMO1 K37Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] SUMO1 K37Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] SUMO1 K37Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM SUMO1 K37Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
5ELJ Isoform-specific inhibition of SUMO-dependent protein-protein interactions Deposited 2015-11-04	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 18–97（80 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M Hepes sodium salt, 10% w/v polyethylene glycol 20000	Resolution 1.98 Å R-free 0.236
5ELJ Isoform-specific inhibition of SUMO-dependent protein-protein interactions Deposited 2015-11-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–97（80 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.1 M Hepes sodium salt, 10% w/v polyethylene glycol 20000	Resolution 1.98 Å R-free 0.236
5GHD SOLUTION STRUCTURE OF LYS39 ACETYLATED HUMAN SUMO1 Deposited 2016-06-19	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 1–97（97 aa） Fragment：UNP RESIDUES 1-97	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；290 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure AMBIENT ATM NMR sample composition 1 mM [U-100% 13C; U-100% 15N] SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 10 mg/mL Pf1 phage, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM SUMO1 K39Ac, 10 mM potassium phosphate, 100 mM potassium chloride, 2 mM DTT, 0.1 mM EDTA, 0.001 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6J4I A conserved and buried edge-to-face aromatic interaction in SUMO is vital for the SUMO pathway Deposited 2019-01-09	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 1–97（97 aa）	Mutation：F64L	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 172；Pressure 1 NMR sample composition 0.5 mM [U-98% 15N] Small Ubiquitin Like Modifier, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6K5T Complex of SUMO1 and phosphorylated hcmv protein IE2 Deposited 2019-05-31	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 21–97（77 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 162.7；Pressure 1 NMR sample composition 0.3 mM [U-13C; U-15N] SUMO1, 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-13C; U-15N] SUMO1, 1.5 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 3 mM Phosphorylated SIM from viral protein IE2, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6UYO Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.64 Å R-free 0.196
6UYO Crystal structure of K37-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14	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 C 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.64 Å R-free 0.196
6UYP Crystal structure of K39-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.42 Å R-free 0.172
6UYQ Crystal structure of K45-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.50 Å R-free 0.175
6UYR Crystal structure of K46-acetylated SUMO1 in complex with PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.30 Å R-free 0.173
6UYS Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.59 Å R-free 0.202
6UYS Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14	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 C 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.59 Å R-free 0.202
6UYT Crystal structure of K39-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.66 Å R-free 0.200
6UYU Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.66 Å R-free 0.186
6UYU Crystal structure of K45-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14	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 C 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.66 Å R-free 0.186
6UYV Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated PML-SIM Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 16% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.40 Å R-free 0.179
6UYX Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated DAXX Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.70 Å R-free 0.210
6UYX Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated DAXX Deposited 2019-11-14	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 C 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.70 Å R-free 0.210
6UYY Crystal structure of K39-acetylated SUMO1 in complex with phosphorylated DAXX Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.60 Å R-free 0.175
6UYZ Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated DAXX Deposited 2019-11-14	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 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.40 Å R-free 0.181
6UYZ Crystal structure of K46-acetylated SUMO1 in complex with phosphorylated DAXX Deposited 2019-11-14	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 C 17–97（81 aa）	Mutation：C52A 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；298 K；100MM SODIUM CACODYLATE PH6.5, 26% PEG3350, 10MM CALCIUM CHLORIDE	Resolution 1.40 Å R-free 0.181
6V7P Crystal structure of SUMO1 in complex with PIAS-SIM2 Deposited 2019-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 17–97（81 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.40 Å R-free 0.184
6V7P Crystal structure of SUMO1 in complex with PIAS-SIM2 Deposited 2019-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–97（81 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.40 Å R-free 0.184
6V7Q Crystal structure of SUMO1 in complex with phosphorylated PIAS-SIM2 Deposited 2019-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 17–97（81 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31% (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.35 Å R-free 0.196
6V7Q Crystal structure of SUMO1 in complex with phosphorylated PIAS-SIM2 Deposited 2019-12-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 17–97（81 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31% (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.35 Å R-free 0.196
6V7R Crystal structure of K37-acetylated SUMO1 in complex with PIAS-SIM2 Deposited 2019-12-09	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 C 17–97（81 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；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.55 Å R-free 0.221
6V7R Crystal structure of K37-acetylated SUMO1 in complex with PIAS-SIM2 Deposited 2019-12-09	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 A 17–97（81 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；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.55 Å R-free 0.221
6V7S Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated PIAS-SIM2 Deposited 2019-12-09	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 C 17–97（81 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；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.47 Å R-free 0.193
6V7S Crystal structure of K37-acetylated SUMO1 in complex with phosphorylated PIAS-SIM2 Deposited 2019-12-09	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 A 17–97（81 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；298 K；100 mM sodium cacodylate pH 6.5, 19 to 31 % (w/v) PEG3350 and 10 mM calcium chloride.	Resolution 1.47 Å R-free 0.193
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–7（6 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000	Resolution 2.10 Å R-free 0.227
6WW3 Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail Deposited 2020-05-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–7（6 aa） Fragment：fusion protein	Not recorded	ZN ZINC ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.2 M ammonium chloride, 0.1 M Tris, pH 8.0 and 20% PEG 6000	Resolution 2.10 Å R-free 0.227
6XOG Structure of SUMO1-ML786519 adduct bound to SAE Deposited 2020-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–101（101 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 1 VAY {(1R,2R,3S,4R)-4-[(5-{4-[(1S)-1-(6-bromopyridin-2-yl)-1-hydroxyethyl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2,3-dihydroxycyclopentyl}methyl sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM BisTris, pH 6.5, 50 mM Ammonium Sulfate, 30% pentaerythritol ethoxylate (Hampton Index 57)	Resolution 1.98 Å R-free 0.240
6XOH Structure of SUMO1-ML00789344 adduct bound to SAE Deposited 2020-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–101（101 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 1 VB7 {(1R,2S,4R)-4-[(5-{4-[(1R)-3,4-dihydro-1H-2-benzopyran-1-yl]thiophene-2-carbonyl}pyrimidin-4-yl)amino]-2-hydroxycyclopentyl}methyl sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM BisTris, pH 6.5, 50 mM Ammonium Sulfate, 30% pentaerythritol ethoxylate (Hampton Index 57)	Resolution 2.23 Å R-free 0.244
6XOI Structure of SUMO1-ML00752641 adduct bound to SAE Deposited 2020-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–101（101 aa）	Not recorded	SO4 SULFATE ION × 1 ZN ZINC ION × 1 VBA [(1R,2R,3S,4R)-4-{[5-(1-benzyl-1H-pyrazole-3-carbonyl)pyrimidin-4-yl]amino}-2,3-dihydroxycyclopentyl]methyl sulfamate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM BisTris, pH 6.5, 50 mM Ammonium Sulfate, 30% pentaerythritol ethoxylate (Hampton Index 57)	Resolution 2.00 Å R-free 0.287
8DJH Ternary complex of SUMO1 with a phosphomimetic SIM of PML and zinc Deposited 2022-06-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–97（96 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride	Resolution 1.77 Å R-free 0.243
8DJI Ternary complex of SUMO1 with the SIM of PML and zinc Deposited 2022-06-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–97（96 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；100 mM HEPES pH 7.0, 19 to 31 % (w/v) PEG 3350, and 1-5 mM zinc chloride	Resolution 1.97 Å R-free 0.258
8ODR Mimetic of UBC9-SUMO1 Deposited 2023-03-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 18–97（80 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；LiSO4, Tris pH8.5, PEG 4000	Resolution 2.85 Å R-free 0.258
9B62 Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model Deposited 2024-03-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain D 1–97（97 aa）	Mutation：Q94P	GTP GUANOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM Tris-Cl pH 8.0, 50 mM NaCl, 0.1 mM TCEP supplemented with 0.02% (v/v) IGEPAL CA-630 cryo-EM vitrification conditions Cryogen ETHANE；30 s wait time, blot for 2.5 s before plunging	Resolution 2.90 Å
9DQB Cryo-EM structure of a double-loaded SUMO E1-E2-SUMO1 complex. Deposited 2024-09-23	Different construct Different mutation/modification 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 D 1–97（97 aa） Chain G 1–97（97 aa）	Mutation：C52A	AMP ADENOSINE MONOPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9DRJ Cryo-EM structure of a SUMO E1-E2-SUMO1 complex. Deposited 2024-09-25	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–97（97 aa）	Not recorded	ZN ZINC ION × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9GNV Human SENP5 in complex with SUMO1 Deposited 2024-09-04	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 B 19–96（78 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；291 K；2.1 M Malic Ac., pH 7.0	Resolution 2.18 Å R-free 0.259
9GNX Human SENP5 in complex with SUMO1 (E67D) Deposited 2024-09-04	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 B 19–96（78 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；291 K；0.2 M LiSO4, 8% PEG2000, 8% PEG500MME, 0.1 M NaAcetate pH 5.5	Resolution 1.90 Å R-free 0.258
9Q9E Crystal structure of a TELSAM-SUMO1 fusion protein Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 18–97（80 aa）	Mutation：V73E	1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Na-phosphate/citric acid pH4.2, PEG600	Resolution 2.05 Å R-free 0.231
9Q9E Crystal structure of a TELSAM-SUMO1 fusion protein Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 18–97（80 aa）	Mutation：V73E	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Na-phosphate/citric acid pH4.2, PEG600	Resolution 2.05 Å R-free 0.231
9Q9E Crystal structure of a TELSAM-SUMO1 fusion protein Deposited 2025-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 18–97（80 aa）	Mutation：V73E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Na-phosphate/citric acid pH4.2, PEG600	Resolution 2.05 Å R-free 0.231
9QTG Simkania negevensis CE-clan virulence factor SnCE1 in complex with hsSUMO1 Deposited 2025-04-08	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 B 20–96（77 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1 CA CALCIUM ION × 1 AYE prop-2-en-1-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M calcium acetate, 20% PEG3350	Resolution 1.55 Å R-free 0.216

62 other PDB entries and 93 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUMO1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–97； UniProt 1–97

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	9lhp
Deposition date deposition_date	2025-01-13
最后修订 last_revision	2026-03-11
Structure title title	Crystal structure of human thymine DNA glycosylase TDG in complex with a covalent inhibitor (1S, 5R)-C-2711
Keywords keywords	Human thymine DNA glycosylase, TDG, Covalent inhibitor, DNA BINDING PROTEIN-INHIBITOT COMPLEX, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	21.26 Å
Radius of gyration Rg (electron density) rg_electron	20.51 Å
Forward intensity I(0) i0	35815800.00
Molecular weight molecular_weight	31036.0 kDa
Excluded volume excluded_volume	30103 Å³
Envelope volume envelope_volume	49935 Å³
Hydration-shell volume shell_volume	20729 Å³
Envelope diameter envelope_diameter	72.8 Å
Shell Rg shell_rg	26.74 Å
Envelope Rg envelope_rg	20.72 Å
Shape Rg shape_rg	20.49 Å
Total Rg total_rg	21.17 Å
Total atoms total_atoms	2349
Residues n_residues	289
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	72.1 Å
Rg (real space) rg_real	21.27 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	3.5820e+07
I(0) uncertainty (real space) i0_real_error	4.4710e+05
Rg (reciprocal space) rg_reciprocal	21.27 Å
I(0) (reciprocal space) i0_reciprocal	35820000.0000
Solution quality estimate total_estimate	0.8755
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	-0.254
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7766000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.804; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	G/T mismatch-specific thymine DNA glycosylase
Molecular weight formula_weight	24434.3 kDa
EC 编号 ec_number	3.2.2.29
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	2444

AELLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCIYEIFSKEVFGVKVKNLEFGLQPHKIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNMDVQEVQYTFDLQLAQEDAKKMAVK

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	Small ubiquitin-related modifier 1
Molecular weight formula_weight	11149.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSDQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFEGQRIADNHTPKELGMEEEDVIEVYQEQTGG

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 3 Entity 3 non-polymer

Description description	(1~{S},2~{S})-2-[(2-methoxy-5-methyl-4-oxidanyl-phenyl)methyl]cyclopropane-1-carboxylic acid
Molecular weight formula_weight	236.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

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8. Citations (1)

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Unit-cell length a length_a	42.697 Å
Unit-cell length b length_b	73.960 Å
Unit-cell length c length_c	109.472 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	2.140 Å
Low-resolution limit resolution_low	27.950 Å
R factor r_factor	0.2077
R_work r_work	0.2057
R_free r_free	0.2426

fit	/app/data/saxs_computation/lh/9lhp/9lhp.fit
pddf	/app/data/pr_computation/lh/9lhp/9lhp.pr.out
profile	/app/data/saxs_computation/lh/9lhp/9lhp.dat

Crystal structure of human thymine DNA glycosylase TDG in complex with a covalent inhibitor (1S, 5R)-C-2711

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

G/T mismatch-specific thymine DNA glycosylase

State in the Current Structure

Other States of the Same Protein in the Database

Small ubiquitin-related modifier 1

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)