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8odr

Mimetic of UBC9-SUMO1

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SUMO-conjugating enzyme UBC9

Homo sapiens

UniProt P63279

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 2–158 Mutation：K14R, A129K Small ubiquitin-related modifier 1 × 1 （P63165） 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

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 8ODR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A3S HUMAN UBC9 Deposited 1998-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；pH 7.
Resolution 2.80 Å R-free 0.260
1KPS Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1 Deposited 2002-01-02 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 1–158（158 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.0M ammonium phosphate, 0.1M hepes, 10mM CuCl2, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.300
1KPS Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin conjugating enzyme Ubc9 and RanGAP1 Deposited 2002-01-02 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 1–158（158 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；2.0M ammonium phosphate, 0.1M hepes, 10mM CuCl2, 5% glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.50 Å R-free 0.300
1Z5S Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2 Deposited 2005-03-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–158（158 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
2GRN Crystal Structure of human RanGAP1-Ubc9 Deposited 2006-04-24 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 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.80 Å R-free 0.218
2GRO Crystal Structure of human RanGAP1-Ubc9-N85Q Deposited 2006-04-24 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 1–158（158 aa）
Mutation：N85Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.202
2GRP Crystal Structure of human RanGAP1-Ubc9-Y87A Deposited 2006-04-24 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 1–158（158 aa）
Mutation：Y87A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.05 Å R-free 0.231
2GRQ Crystal Structure of human RanGAP1-Ubc9-D127A Deposited 2006-04-24 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 1–158（158 aa）
Mutation：D127A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.70 Å R-free 0.205
2GRR Crystal Structure of human RanGAP1-Ubc9-D127S Deposited 2006-04-24 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 1–158（158 aa）
Mutation：D127S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；1M lithium sulfate, 0.5M ammonium sulfate, 50mM sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.30 Å R-free 0.222
2O25 Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9 Deposited 2006-11-29 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 D 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.291
2O25 Ubiquitin-Conjugating Enzyme E2-25 kDa Complexed With SUMO-1-Conjugating Enzyme UBC9 Deposited 2006-11-29 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 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；The protein complex (1:1) was dissolved at 26 mg/ml in 20 mM Tris-HCl, pH 8.0, 5% glycerol, 2 mM DTT. Hanging drops (2 microL + 2 microL), room temperature, well solution: 16% PEG MME 5000, 0.1 M bis-Tris, pH 6.0, 1 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.60 Å R-free 0.291
2PE6 Non-covalent complex between human SUMO-1 and human Ubc9 Deposited 2007-04-02 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 1–158（158 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
2PX9 The intrinsic affinity between E2 and the Cys domain of E1 in Ubiquitin-like modifications Deposited 2007-05-14 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–158（158 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 50mM Phosphate；Pressure 1
NMR sample composition 0.15-0.6mM E1 Cys domain, 0.15-0.7mM Ubc9, 50mM Phosphate buffer | 50mM Phosphate buffer
Resolution not provided
2XWU CRYSTAL STRUCTURE OF IMPORTIN 13 - UBC9 COMPLEX Deposited 2010-11-05 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 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；50 MM MES PH 6.5 25% PEG 300
Resolution 2.80 Å R-free 0.268
3A4S The crystal structure of the SLD2:Ubc9 complex Deposited 2009-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.269
3A4S The crystal structure of the SLD2:Ubc9 complex Deposited 2009-07-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；25% polyethylene glycol 1500, 0.1M SPG buffer : SPG buffer was prepared by mixing succinic acid, sodium dihydrogen phosphate, and glycine in the molar ratios 2:7:7, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.269
3UIN Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 Deposited 2011-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；279 K；100 mM HEPES pH 7.5, 400 mM ammonium citrate, 2% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.60 Å R-free 0.264
3UIO Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–158（158 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；14% PEG4000, 100 mM sodium citrate pH 6.0, 200 mM ammonium acetate, vapor diffusion, hanging drop, temperature 279K
Resolution 2.60 Å R-free 0.251
3UIP Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II Deposited 2011-11-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–158（158 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；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
4W5V Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with E1-activating enzyme (Uba2) ubiquitin fold domain (Ufd) Deposited 2014-08-19 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 1–158（158 aa）
Not recorded FMT FORMIC ACID × 1 GOL GLYCEROL × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；100 mM Tris, pH 8.0, 20% PEG MME 550, 200 mM potassium formate, 20% glycerol; seeded
Resolution 2.50 Å R-free 0.283
4Y1L Ubc9 Homodimer The Missing Link in Poly-SUMO Chain Formation Deposited 2015-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–158（158 aa）
Chain B 1–158（158 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8；293 K；10% (w/v) PEG8000, 100 mM HEPES, pH 8.0, 8% ethylene glycol
Resolution 2.70 Å R-free 0.278
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–158（158 aa）
Mutation：K14R EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5
Resolution 2.40 Å R-free 0.234
5D2M Complex between human SUMO2-RANGAP1, UBC9 and ZNF451 Deposited 2015-08-05 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 1–158（158 aa）
Mutation：K14R EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；6 % (w/v) PEG 8000, 0.2 M ammonium citrate and 0.1 M HEPES pH 7.5
Resolution 2.40 Å R-free 0.234
5F6D Crystal structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 6 Deposited 2015-12-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,E54A 5VJ 6~{H}-benzo[c][1,2]benzothiazine 5,5-dioxide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Resolution 1.55 Å R-free 0.196
5F6E Crystal Structure of human Ubc9 (K48A/K49A/E54A) Deposited 2015-12-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,E54A EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol
Resolution 1.12 Å R-free 0.170
5F6U Crystal Structure of Ubc9 (K48A/K49A/E54A) complexed with Fragment 8 (JSS190B146) Deposited 2015-12-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,K54A 5VK ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol
Resolution 1.55 Å R-free 0.203
5F6V Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol from fragment cocktail screen) Deposited 2015-12-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,E54A 5VL 2-(2-hydroxyphenyl)phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Resolution 1.49 Å R-free 0.184
5F6W Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 1 (biphenol) Deposited 2015-12-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,E54A 5VL 2-(2-hydroxyphenyl)phenol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol
Resolution 1.70 Å R-free 0.200
5F6X Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole from cocktail screen) Deposited 2015-12-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,E54A 5VM 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Resolution 1.56 Å R-free 0.193
5F6Y Crystal structure of Ubc9 (K48/K49A/E54A) complexed with Fragment 2 (mercaptobenzoxazole) Deposited 2015-12-07 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–158（157 aa）
Mutation：K48A,K49A,E54A 5VM 5-chloranyl-3~{H}-1,3-benzoxazole-2-thione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；294 K；0.1M Tris pH 8.5, 8% (w/v) polyethylene glycol 8000
Resolution 1.14 Å R-free 0.178
5FQ2 Crystal structure of human SUMO E1 UFD domain in complex with Ubc9 in a P422 space group. Deposited 2015-12-04 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 A 1–158（158 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.249
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–158（157 aa）
Mutation：K48A, K49A, E54A, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000
Resolution 1.90 Å R-free 0.263
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–158（157 aa）
Mutation：K48A, K49A, E54A, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000
Resolution 1.90 Å R-free 0.263
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 2–158（157 aa）
Mutation：K48A, K49A, E54A, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000
Resolution 1.90 Å R-free 0.263
6SYF Human Ubc9 with covalent isopeptide ligand Deposited 2019-09-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 2–158（157 aa）
Mutation：K48A, K49A, E54A, C138A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293.15 K；0.1 M trisodium citrate pH 5.0, 30% PEG8000
Resolution 1.90 Å R-free 0.263
9B62 Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model Deposited 2024-03-23 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 × 7 PDB declaration: heptameric
Chain C 1–158（158 aa）
Not recorded 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 C 1–158（158 aa）
Mutation：F22A,G23Q,V25S,A129K,C138S,K153R 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 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 × 4 PDB declaration: tetrameric
Chain C 1–158（158 aa）
Mutation：C138S 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
9GLR Crystal Structure of Human UBC9 C93E Deposited 2024-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 1–158（158 aa）
Mutation：C93E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；2% tacsimate, pH 5.0, 0.1 M sodium citrate, 16% PEG 3350
Resolution 1.72 Å R-free 0.227

32 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBC9_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 9–165； UniProt 2–158

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 18–97 Not recorded SUMO-conjugating enzyme UBC9 × 1 （P63279） 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

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 8ODR 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 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 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 construct 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 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 1–97（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 construct 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 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 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 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）
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 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）
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 construct 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 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 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 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 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 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 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 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）
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
9B62 Human RANBP2/RAN(GTP)/RANGAP1-SUMO1/UBC9/CRM1/RAN(GTP) - composite map and model Deposited 2024-03-23 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 × 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 construct 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
9LHP Crystal structure of human thymine DNA glycosylase TDG in complex with a covalent inhibitor (1S, 5R)-C-2711 Deposited 2025-01-13 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–97（97 aa）
Not recorded 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
9Q9E Crystal structure of a TELSAM-SUMO1 fusion protein Deposited 2025-02-26 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 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 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 11–90； UniProt 18–97

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

SAXS profile for 8odr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8odr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8odr
Deposition date deposition_date2023-03-09
Structure title titleMimetic of UBC9-SUMO1
Keywords keywordsUBC9, SUMO1, CONJUGATION, UBIQUITIN-LIKE, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.10 Å
Radius of gyration Rg (electron density) rg_electron22.57 Å
Forward intensity I(0) i011587100.00
Molecular weight molecular_weight25385.0 kDa
Excluded volume excluded_volume31649 ų
Envelope volume envelope_volume39224 ų
Hydration-shell volume shell_volume16143 ų
Envelope diameter envelope_diameter78.3 Å
Shell Rg shell_rg27.10 Å
Envelope Rg envelope_rg22.65 Å
Shape Rg shape_rg22.54 Å
Total Rg total_rg23.29 Å
Total atoms total_atoms1788
Residues n_residues233
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax78.8 Å
Rg (real space) rg_real23.31 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real1.1590e+07
I(0) uncertainty (real space) i0_real_error1.8130e+05
Rg (reciprocal space) rg_reciprocal23.26 Å
I(0) (reciprocal space) i0_reciprocal11590000.0000
Solution quality estimate total_estimate0.8337
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.4 Å
Skewness Skewness skewness0.514
Kurtosis Kurtosis kurtosis-0.370
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3079000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.737; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.688; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)