Current Protein Identity:P22515 New Search
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3CMM Crystal Structure of the Uba1-Ubiquitin Complex Deposited 2008-03-23 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 5 PDB declaration: pentameric(5) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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
6ZHS Uba1 bound to two E2 (Ubc13) molecules Deposited 2020-06-23 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
Chain A 1–1024(1024 aa)
Not recorded 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
6ZHT Uba1-Ubc13 disulfide mediated complex Deposited 2020-06-23 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 2 PDB declaration: dimeric(2) Consistent with protein count
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 Assembly 1 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 2 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 3 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 4 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 5 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 6 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 7 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 8 Protein heterocomplex Heteromer;Protein × 3 PDB declaration: trimeric(3) Consistent with protein count
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 Assembly 1 Protein monomer Monomer;Protein × 1 PDB declaration: monomeric(1) Consistent with protein count
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