6nya

Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin

Method: X-RAY DIFFRACTION D_max: 152.3 Å Quality: GOOD

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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)

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 11–1024	Fragment：residues 11-1024	Ubiquitin × 1 （A0A1D6RLC6） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 11–1024	Fragment：residues 11-1024	Ubiquitin × 1 （A0A1D6RLC6） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） 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

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 6NYA	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 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 1–1024（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 construct 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 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 1–1024（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 construct 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 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 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 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 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
6ZHS Uba1 bound to two E2 (Ubc13) molecules Deposited 2020-06-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	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	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 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 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 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 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 construct 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 construct 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 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 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 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 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 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 28 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 4–1017； UniProt 11–1024 Author chain D； PDBConstruct 4–1017； UniProt 11–1024

Ubiquitin

Triticum aestivum

UniProt A0A1D6RLC6

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 77–152	Fragment：residues 77-152 Mutation：K6R, K11R, K27R, K29R, K33R, K48R, K63R	Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain E； UniProt 77–152	Fragment：residues 77-152 Mutation：K6R, K11R, K27R, K29R, K33R, K48R, K63R	Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） 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

Other States of the Same Protein in the Database

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

View Construct and Data Evidence

UniProt name	A0A1D6RLC6_WHEAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 10–85； UniProt 77–152 Author chain E； PDBConstruct 10–85； UniProt 77–152

Ubiquitin-conjugating enzyme E2-34 kDa

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P14682

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 C； UniProt 3–195	Fragment：residues 3-195	Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin × 1 （A0A1D6RLC6） 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
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 3–195	Fragment：residues 3-195	Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin × 1 （A0A1D6RLC6） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6NYA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6NYD Crystal Structure of S. cerevisiae Ubc3 (Cdc34) Deposited 2019-02-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 3–195（193 aa） Fragment：residues 3-195	Not recorded	ZN ZINC ION × 4 ACT ACETATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.06 M zinc acetate, 0.108mM sodium cacodylate, 14.4% PEG 8,000, 20% glycerol	Resolution 1.65 Å R-free 0.199
6ZHU Yeast Uba1 in complex with Ubc3 and ATP 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 B 1–295（295 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 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 F 1–295（295 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–295（295 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 construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–295（295 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
7K5J Structure of an E1-E2-ubiquitin thioester mimetic Deposited 2020-09-16	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 J 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain T 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain V 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 3–195（193 aa）	Mutation：A141K	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 3–195（193 aa）	Mutation：A141K	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

3 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBC3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–197； UniProt 3–195 Author chain F； PDBConstruct 5–197； UniProt 3–195

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6nya
Deposition date deposition_date	2019-02-11
Structure title title	Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin
Keywords keywords	;CONFORMATIONAL CHANGE, THIOESTER, ADENYLATION, THIOESTER TRANSFER, TRANSTHIOESTERIFICATION, ATP-BINDING, UBIQUITIN E2-BINDING, UBIQUITINATION, LIGASE, LIGASE-TRANSFERASE complex ;; LIGASE/TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.93 Å
Radius of gyration Rg (electron density) rg_electron	44.80 Å
Forward intensity I(0) i0	1145760000.00
Molecular weight molecular_weight	281200.0 kDa
Excluded volume excluded_volume	352180 Å³
Envelope volume envelope_volume	471400 Å³
Hydration-shell volume shell_volume	85534 Å³
Envelope diameter envelope_diameter	167.9 Å
Shell Rg shell_rg	50.80 Å
Envelope Rg envelope_rg	44.82 Å
Shape Rg shape_rg	44.81 Å
Total Rg total_rg	45.01 Å
Total atoms total_atoms	19796
Residues n_residues	2466
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	152.3 Å
Rg (real space) rg_real	44.93 Å
Rg uncertainty (real space) rg_real_error	1.65 Å
I(0) (real space) i0_real	1.1460e+09
I(0) uncertainty (real space) i0_real_error	2.2700e+07
Rg (reciprocal space) rg_reciprocal	44.93 Å
I(0) (reciprocal space) i0_reciprocal	1146000000.0000
Solution quality estimate total_estimate	0.8679
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.2 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.222
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	201800000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.809; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.858

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-activating enzyme E1 1
Molecular weight formula_weight	113704.2 kDa
EC 编号 ec_number	6.2.1.45
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	20705

GAMAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPNKIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDPNANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	9821.1 kDa
Mutation mutation	K6R, K11R, K27R, K29R, K33R, K48R, K63R
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MHHHHHHGAMQIFVRTLTGRTITLEVESSDTIDNVRARIQDREGIPPDQQRLIFAGRQLEDGRTLADYNIQRESTLHLVLRLRGG

来源 Source

来源生物 organism	Triticum aestivum
通用名 common_name	Wheat
NCBI Class编号 ncbi_taxonomy_id	4565
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Ubiquitin-conjugating enzyme E2-34 kDa
Molecular weight formula_weight	22427.2 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GAMASRKSTASSLLLRQYRELTDPKKAIPSFHIELEDDSNIFTWNIGVMVLNEDSIYHGGFFKAQMRFPEDFPFSPPQFRFTPAIYHPNVYRDGRLCISILHQSGDPMTDEPDAETWSPVQTVESVLISIVSLLEDPNINSPANVDAAVDYRKNPEQYKQRVKMEVERSKQDIPKGFIMPTSESAYISQSKLDEPES

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	nat
Copy count entity_count	21

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	909

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7. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6nyab1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6nyab2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nyac_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d6nyae1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d6nyae2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6nyaf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

CATH v4.4 (16 domains)

Domain ID domain_id	6nyaA01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	80 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1

Domain ID domain_id	6nyaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12550 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2

Domain ID domain_id	6nyaA03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	180 — Ubiquitin-activating enzyme E1, FCCH domain

Domain ID domain_id	6nyaA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	6nyaA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2660 — Ubiquitin-activating enzyme E1, SCCH domain

Domain ID domain_id	6nyaA06
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily	60 — Ubiquitin-activating enzyme E1, UFD domain

Domain ID domain_id	6nyaB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6nyaC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	6nyaD01
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily	80 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1

Domain ID domain_id	6nyaD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	12550 — Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 2

Domain ID domain_id	6nyaD03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	180 — Ubiquitin-activating enzyme E1, FCCH domain

Domain ID domain_id	6nyaD04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	6nyaD05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2660 — Ubiquitin-activating enzyme E1, SCCH domain

Domain ID domain_id	6nyaD06
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily	60 — Ubiquitin-activating enzyme E1, UFD domain

Domain ID domain_id	6nyaE01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	6nyaF00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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8. Citations (1)

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Unit-cell length a length_a	126.445 Å
Unit-cell length b length_b	68.544 Å
Unit-cell length c length_c	171.721 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.72 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.065 Å
Low-resolution limit resolution_low	117.035 Å
R factor r_factor	0.1875
R_work r_work	0.1872
R_free r_free	0.2168

fit	/app/data/saxs_computation/ny/6nya/6nya.fit
pddf	/app/data/pr_computation/ny/6nya/6nya.pr.out
profile	/app/data/saxs_computation/ny/6nya/6nya.dat

Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin

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

Ubiquitin-activating enzyme E1 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-conjugating enzyme E2-34 kDa

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (6 domains)

CATH v4.4 (16 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)