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6zhs

Uba1 bound to two E2 (Ubc13) molecules

Method: X-RAY DIFFRACTION Dmax: 108.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ubiquitin-activating enzyme E1 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P22515

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 1–1024 Not recorded Ubiquitin-conjugating enzyme E2 13 × 2 （P52490） SO4 SULFATE ION × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；273 K；ammonium sulfate, HEPES, PEG 3350 Resolution 2.35 Å R-free 0.275

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 6ZHS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 10–1024（1015 aa） Fragment：Residues 10-1024
Not recorded PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.247
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 10–1024（1015 aa） Fragment：Residues 10-1024
Not recorded PRO PROLINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；L-proline, PEG 5000 MME, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.70 Å R-free 0.247
4NNJ Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified ubiquitin Deposited 2013-11-18 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 9–1024（1016 aa） Fragment：UNP residues 9-1024
Chain C 9–1024（1016 aa） Fragment：UNP residues 9-1024
Not recorded SO4 SULFATE ION × 4 GOL GLYCEROL × 29 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；15% (w/v) polyethylene glycol 3350, 100mM lithium sulfate and 100mM BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.201
5L6H Uba1 in complex with Ub-ABPA3 covalent adduct Deposited 2016-05-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 CL CHLORIDE ION × 4 GOL GLYCEROL × 7 6O2 [(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Resolution 2.30 Å R-free 0.218
5L6H Uba1 in complex with Ub-ABPA3 covalent adduct Deposited 2016-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 CL CHLORIDE ION × 4 GOL GLYCEROL × 4 6O2 [(2~{R},3~{S},4~{R},5~{R})-5-[6-[(3-ethynylphenyl)amino]purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl sulfamate × 1 MG MAGNESIUM ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Resolution 2.30 Å R-free 0.218
5L6I Uba1 in complex with Ub-MLN4924 covalent adduct Deposited 2016-05-30 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 CL CHLORIDE ION × 8 GOL GLYCEROL × 9 B39 [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Resolution 2.76 Å R-free 0.220
5L6I Uba1 in complex with Ub-MLN4924 covalent adduct Deposited 2016-05-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–1024（1024 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 1 CL CHLORIDE ION × 8 GOL GLYCEROL × 7 B39 [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Resolution 2.76 Å R-free 0.220
5L6J Uba1 in complex with Ub-MLN7243 covalent adduct Deposited 2016-05-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1024（1024 aa）
Not recorded SO4 SULFATE ION × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 7 61T [(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Resolution 2.68 Å R-free 0.224
5L6J Uba1 in complex with Ub-MLN7243 covalent adduct Deposited 2016-05-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–1024（1024 aa）
Not recorded SO4 SULFATE ION × 1 CL CHLORIDE ION × 2 GOL GLYCEROL × 9 61T [(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.2M lithium sulfate, 0.1M bis-tris, 15% peg 3350
Resolution 2.68 Å R-free 0.224
5TR4 Structure of Ubiquitin activating enzyme (Uba1) in complex with ubiquitin and TAK-243 Deposited 2016-10-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 9–1024（1016 aa） Fragment：residues 9-1024
Mutation：N471M, K519R 61T [(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；70 mM Na malonate pH 6.0, 70 mM malic acid, 70 mM Na citrate, 10-15% peg-3350
Resolution 2.20 Å R-free 0.256
5TR4 Structure of Ubiquitin activating enzyme (Uba1) in complex with ubiquitin and TAK-243 Deposited 2016-10-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 9–1024（1016 aa） Fragment：residues 9-1024
Mutation：N471M, K519R 61T [(1~{R},2~{R},3~{S},4~{R})-2,3-bis(oxidanyl)-4-[[2-[3-(trifluoromethylsulfanyl)phenyl]pyrazolo[1,5-a]pyrimidin-7-yl]amino]cyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；70 mM Na malonate pH 6.0, 70 mM malic acid, 70 mM Na citrate, 10-15% peg-3350
Resolution 2.20 Å R-free 0.256
6NYA Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin Deposited 2019-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 11–1024（1014 aa） Fragment：residues 11-1024
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M ammonium sulfate, 25% PEG 3,350, 0.1 M Bis-Tris pH 6.5
Resolution 2.06 Å R-free 0.217
6NYA Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin Deposited 2019-02-11 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 11–1024（1014 aa） Fragment：residues 11-1024
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.2 M ammonium sulfate, 25% PEG 3,350, 0.1 M Bis-Tris pH 6.5
Resolution 2.06 Å R-free 0.217
6ZHT Uba1-Ubc13 disulfide mediated complex Deposited 2020-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 25–1024（1000 aa）
Not recorded GOL GLYCEROL × 12 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；273 K；ammonium nitrate, CHES, PEG 4000
Resolution 2.30 Å R-free 0.263
6ZHU Yeast Uba1 in complex with Ubc3 and ATP Deposited 2020-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1024（1024 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium chloride, PEG 3350
Resolution 3.18 Å R-free 0.263
6ZHU Yeast Uba1 in complex with Ubc3 and ATP Deposited 2020-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–1024（1024 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium chloride, PEG 3350
Resolution 3.18 Å R-free 0.263
6ZHU Yeast Uba1 in complex with Ubc3 and ATP Deposited 2020-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–1024（1024 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium chloride, PEG 3350
Resolution 3.18 Å R-free 0.263
6ZHU Yeast Uba1 in complex with Ubc3 and ATP Deposited 2020-06-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1–1024（1024 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium chloride, PEG 3350
Resolution 3.18 Å R-free 0.263
6ZQH Yeast Uba1 in complex with ubiquitin Deposited 2020-07-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1024（1024 aa）
Not recorded BME BETA-MERCAPTOETHANOL × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium formate, PEG 3350
Resolution 2.03 Å R-free 0.227
6ZQH Yeast Uba1 in complex with ubiquitin Deposited 2020-07-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–1024（1024 aa）
Not recorded BME BETA-MERCAPTOETHANOL × 2 GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；ammonium formate, PEG 3350
Resolution 2.03 Å R-free 0.227
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain S 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain U 11–1024（1014 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 11–1024（1014 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.91；291 K；0.2 M NH4Ac, pH 6.91, 20% PEG3350, 0.02% (+/-)-2-Methyl-2,4-pentanediol, 0.02% 1,2,3,-Heptanetriol, 0.02% Diethylenetriaminepentakis (methylphosphonic acid), 0.02% D-Sorbitol, 0.02% Glycerol, 0.002 M HEPES sodium pH 6.8
Resolution 3.42 Å R-free 0.246
7ZH9 Uba1 in complex with ATP Deposited 2022-04-05 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 1–1024（1024 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 1 ACT ACETATE ION × 1 MG MAGNESIUM ION × 3 GOL GLYCEROL × 10 K POTASSIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5 and 25% PEG 3350
Resolution 1.72 Å R-free 0.206

12 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBA1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1024； UniProt 1–1024

Ubiquitin-conjugating enzyme E2 13

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P52490

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 1–153 Chain C； UniProt 1–153 Not recorded Ubiquitin-activating enzyme E1 1 × 1 （P22515） SO4 SULFATE ION × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；273 K；ammonium sulfate, HEPES, PEG 3350 Resolution 2.35 Å R-free 0.275

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 6ZHS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JAT Mms2/Ubc13 Ubiquitin Conjugating Enzyme Complex Deposited 2001-05-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–153（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 1000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.60 Å R-free 0.239
1JBB Ubiquitin Conjugating Enzyme, Ubc13 Deposited 2001-06-03 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 1–153（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 5000-MME, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.255
1JBB Ubiquitin Conjugating Enzyme, Ubc13 Deposited 2001-06-03 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 1–153（153 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；PEG 5000-MME, ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.00 Å R-free 0.255
2GMI Mms2/Ubc13~Ubiquitin Deposited 2006-04-06 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–152（152 aa）
Mutation：C87S No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；17% PEG 1000, 100 mM Na/K phosphate, pH 6.2, 25 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.50 Å R-free 0.268
4FH1 S. cerevisiae Ubc13-N79A Deposited 2012-06-05 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 1–153（153 aa）
Mutation：N79A, C87S NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.3；296 K；0.1 M CHES, pH 10.3, 20% PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Resolution 2.61 Å R-free 0.246
5OJW S. cerevisiae UBC13 - MMs2 complex Deposited 2017-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–152（152 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；0.1M Bis-Tris Propane / Citric Acid Buffer, pH 7.6, 20% PEG3000
Resolution 2.00 Å R-free 0.205
6ZHT Uba1-Ubc13 disulfide mediated complex Deposited 2020-06-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–152（152 aa）
Not recorded GOL GLYCEROL × 12 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；273 K；ammonium nitrate, CHES, PEG 4000
Resolution 2.30 Å R-free 0.263
9GLT Crystal Structure of Yeast Ubc13 C87E 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 1–153（153 aa）
Mutation：C87E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000
Resolution 1.45 Å R-free 0.228
9GLT Crystal Structure of Yeast Ubc13 C87E Deposited 2024-08-28 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 BBB 1–153（153 aa）
Mutation：C87E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M sodium cacodylate, pH 6.5, 25% PEG 4000
Resolution 1.45 Å R-free 0.228

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UBC13_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 2–154； UniProt 1–153 Author chain C； PDBConstruct 2–154； UniProt 1–153

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 6zhs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zhs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zhs
Deposition date deposition_date2020-06-23
Structure title titleUba1 bound to two E2 (Ubc13) molecules
Keywords keywordsUbiquitin, E1, Ubc13, 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_guinier34.82 Å
Radius of gyration Rg (electron density) rg_electron33.93 Å
Forward intensity I(0) i0317680000.00
Molecular weight molecular_weight146450.0 kDa
Excluded volume excluded_volume184470 ų
Envelope volume envelope_volume239980 ų
Hydration-shell volume shell_volume57013 ų
Envelope diameter envelope_diameter110.8 Å
Shell Rg shell_rg42.21 Å
Envelope Rg envelope_rg33.49 Å
Shape Rg shape_rg33.93 Å
Total Rg total_rg34.54 Å
Total atoms total_atoms20597
Residues n_residues1297
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 dmax108.8 Å
Rg (real space) rg_real34.64 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real3.1770e+08
I(0) uncertainty (real space) i0_real_error4.7920e+06
Rg (reciprocal space) rg_reciprocal34.76 Å
I(0) (reciprocal space) i0_reciprocal317700000.0000
Solution quality estimate total_estimate0.7086
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary45.9 Å
Skewness Skewness skewness0.153
Kurtosis Kurtosis kurtosis-0.467
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha63410000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.980; Smooth: 0.925
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id6zhsA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id6zhsA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id6zhsB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
Domain ID domain_id6zhsC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily10 — Ubiquitin Conjugating Enzyme
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8. Citations (1)

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9. Files and Curves (10)