3cmm

Crystal Structure of the Uba1-Ubiquitin Complex

Method: X-RAY DIFFRACTION D_max: 157.8 Å Quality: REASONABLE

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

Ubiquitin-activating enzyme E1 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 10–1024	Fragment：Residues 10-1024	Ubiquitin × 1 （P61864） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 10–1024	Fragment：Residues 10-1024	Ubiquitin × 1 （P61864） 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

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 3CMM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 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 oligomeric state 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 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 oligomeric state 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 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 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 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 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 oligomeric state 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 oligomeric state 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
6ZHS Uba1 bound to two E2 (Ubc13) molecules 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 × 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 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 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 1–1015； UniProt 10–1024 Author chain C； PDBConstruct 1–1015； UniProt 10–1024

Ubiquitin

Saccharomyces cerevisiae

UniProt P61864

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–76	Not recorded	Ubiquitin-activating enzyme E1 1 × 1 （P22515） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 1–76	Not recorded	Ubiquitin-activating enzyme E1 1 × 1 （P22515） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3CMM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1OTR Solution Structure of a CUE-Ubiquitin Complex Deposited 2003-03-22	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 7.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 99.996% D2O NMR sample composition 1 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN3 \| 99.996% D2O	Resolution not provided
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex Deposited 2003-07-17	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6.0, 0.2% NaN3；Pressure 1 NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 90% H2O/10% D2O NMR sample composition 1 mM U-15N,13C Ubiquitin + 1 mM Vps27 amino-terminal UIM \| 100% D2O	Resolution not provided
1WR1 The complex structure of Dsk2p UBA with ubiquitin Deposited 2004-10-08	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate, 5mM potassium chloride NMR sample composition U-15N, 13C ubiquitin + DSK2-UBA complex (0.9mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O NMR sample composition U-15N, 13C DSK2-UBA + ubiquitin complex (1.0mM) \| 20mM Phosphate buffer (pH 6.8); 5mM potassium chloride; 1mM EDTA; 5% D2O	Resolution not provided
1ZGU Solution structure of the human Mms2-Ubiquitin complex Deposited 2005-04-22	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Mutation：K48R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 150 mM NaCl；Pressure 1 NMR sample composition [U-15N; U-10% 13C]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20 NMR sample composition [U-13C; U-15N]-Ubiquitin + hMms2 (4:1 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20 NMR sample composition [U-13C; U-15N]-hMms2 + Ubiquitin (1:4 ratio) 90% H20 : 10% D20 \| 90% H20 : 10% D20	Resolution not provided
1ZW7 Elimination of the C-cap in Ubiquitin Structure, Dynamics and Thermodynamic Consequences Deposited 2005-06-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：R42E, E34P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) 30 mM actate；Pressure Ambient NMR sample composition 1-2 mM of appropriately labeled mutant ubiquitin \| 30 mM acetate buffer, pH 5.0	Resolution not provided
2G3Q Solution Structure of Ede1 UBA-ubiquitin complex Deposited 2006-02-20	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM Sodium Phosphate；Pressure 1 NMR sample composition 1mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM 15N,13C-labeled Ede1 UBA; 1mM Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O \| 100% D2O NMR sample composition 1mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 1mM Ede1 UBA; 1mM 15N,13C-labeled Ubiquitin; 20mM phosphate buffer (pH 6.0), 2mM DTT, 0.2% NaN3, 100% D2O \| 100% D2O	Resolution not provided
2JT4 Solution Structure of the Sla1 SH3-3-Ubiquitin Complex Deposited 2007-07-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：SH3 domain sequence database residues 350-420	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；318 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] SH3, 0.9 mM ubiquitin, 100% D2O \| 100% D2O NMR sample composition 0.9 mM [U-98% 13C; U-98% 15N] ubiquitin, 0.9 mM SH3, 100% D2O \| 100% D2O	Resolution not provided
2JWZ Mutations in the hydrophobic core of ubiquitin differentially affect its recognition by receptor proteins Deposited 2007-10-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Mutation：L69S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；296 K；Ionic strength (raw mmCIF value) 20 mM；Pressure AMBIENT NMR sample composition 2 mM [U-100% 15N] L69S UBIQUITIN, 2 mM L69S UBIQUITIN, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2L00 Solution structure of the non-covalent complex of the ZNF216 A20 domain with ubiquitin Deposited 2010-06-29	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：ubiquitin core domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 4 mM ZNF216-A20-1, 50 uM Zinc-2, 0.1 mM DSS-3, 5 mM TRIS-4, 50 mM sodium chloride-5, 1 mM [U-100% 15N] ubiquitin-6, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-7, 50 uM Zinc-8, 4 mM MTSL-9, 5 mM TRIS-10, 50 mM sodium chloride-11, 4 mM ubiquitin-12, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-100% 13C; U-100% 15N] ZNF216-A20-13, 50 uM Zinc-14, 0.1 mM DSS-15, 5 mM TRIS-16, 50 mM sodium chloride-17, 2 mM ubiquitin-18, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1.0 mM [U-100% 15N] ZNF216-A20-19, 50 uM Zinc-20, 0.1 mM DSS-21, 5 mM TRIS-22, 50 mM sodium chloride-23, 5 % Polyacrylamide gel-24, 4 mM ubiquitin-25, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 4 mM ZNF216-A20-26, 50 uM Zinc-27, 0.1 mM DSS-28, 5 mM TRIS-29, 50 mM sodium chloride-30, 5 % Polyacrylamide gel-31, 1 mM [U-100% 15N] ubiquitin-32, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 2 mM ZNF216-A20-33, 50 uM Zinc-34, 0.1 mM DSS-35, 5 mM TRIS-36, 50 mM sodium chloride-37, 1 mM [U-100% 13C; U-100% 15N] ubiquitin-38, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 15N] ZNF216-A20-39, 50 uM Zinc-40, 0.1 mM DSS-41, 5 mM TRIS-42, 50 mM sodium chloride-43, 4 mM ubiquitin-44, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3L0W Structure of split monoubiquitinated PCNA with ubiquitin in position two Deposited 2009-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：ubi-C fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04 M ammonium sulfate, 0.1 M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.314
3L10 Structure of split monoubiquitinated PCNA with ubiquitin in position one Deposited 2009-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–76（76 aa） Fragment：Ubi-C fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；2.04M ammonium sulfate, 0.1M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.314

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBIQ_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76

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	3cmm
Deposition date deposition_date	2008-03-23
Structure title title	Crystal Structure of the Uba1-Ubiquitin Complex
Keywords keywords	;Ubiquitin, E1, Uba1, Protein turnover, ligase, Conformational change, thioester, adenylation, transthioesterification, ATP-binding, Nucleotide-binding, Nucleus, Phosphoprotein, Ubl conjugation pathway, DNA damage, DNA repair, LIGASE-PROTEIN BINDING COMPLEX ;; LIGASE/PROTEIN BINDING
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	43.55 Å
Radius of gyration Rg (electron density) rg_electron	43.32 Å
Forward intensity I(0) i0	834797000.00
Molecular weight molecular_weight	241910.0 kDa
Excluded volume excluded_volume	304370 Å³
Envelope volume envelope_volume	419120 Å³
Hydration-shell volume shell_volume	79103 Å³
Envelope diameter envelope_diameter	174.8 Å
Shell Rg shell_rg	48.93 Å
Envelope Rg envelope_rg	43.58 Å
Shape Rg shape_rg	43.31 Å
Total Rg total_rg	43.61 Å
Total atoms total_atoms	17065
Residues n_residues	2159
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	157.8 Å
Rg (real space) rg_real	43.57 Å
Rg uncertainty (real space) rg_real_error	1.57 Å
I(0) (real space) i0_real	8.3480e+08
I(0) uncertainty (real space) i0_real_error	1.6810e+07
Rg (reciprocal space) rg_reciprocal	43.55 Å
I(0) (reciprocal space) i0_reciprocal	834800000.0000
Solution quality estimate total_estimate	0.6188
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	52.6 Å
Skewness Skewness skewness	0.446
Kurtosis Kurtosis kurtosis	0.043
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	144100000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 1.000; Sysdev: 0.032; Positv: 1.000; Valcen: 0.992; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-activating enzyme E1 1
Molecular weight formula_weight	113516.0 kDa
EC 编号 ec_number	6.3.2.19
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17241

AAGEIDESLYSRQLYVLGKEAMLKMQTSNVLILGLKGLGVEIAKNVVLAGVKSMTVFDPEPVQLADLSTQFFLTEKDIGQKRGDVTRAKLAELNAYVPVNVLDSLDDVTQLSQFQVVVATDTVSLEDKVKINEFCHSSGIRFISSETRGLFGNTFVDLGDEFTVLDPTGEEPRTGMVSDIEPDGTVTMLDDNRHGLEDGNFVRFSEVEGLDKLNDGTLFKVEVLGPFAFRIGSVKEYGEYKKGGIFTEVKVPRKISFKSLKQQLSNPEFVFSDFAKFDRAAQLHLGFQALHQFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELSYQARGDIPGVVAFFGGLVAQEVLKACSGKFTPLKQFMYFDSLESLPDPKNFPRNEKTTQPVNSRYDNQIAVFGLDFQKKIANSKVFLVGSGAIGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNRQFLFRPKDVGKNKSEVAAEAVCAMNPDLKGKINAKIDKVGPETEEIFNDSFWESLDFVTNALDNVDARTYVDRRCVFYRKPLLESGTLGTKGNTQVIIPRLTESYSSSRDPPEKSIPLCTLRSFPNKIDHTIAWAKSLFQGYFTDSAENVNMYLTQPNFVEQTLKQSGDVKGVLESISDSLSSKPHNFEDCIKWARLEFEKKFNHDIKQLLFNFPKDAKTSNGEPFWSGAKRAPTPLEFDIYNNDHFHFVVAGASLRAYNYGIKSDDSNSKPNVDEYKSVIDHMIIPEFTPNANLKIQVNDDDPDPNANAANGSDEIDQLVSSLPDPSTLAGFKLEPVDFEKDDDTNHHIEFITACSNCRAQNYFIETADRQKTKFIAGRIIPAIATTTSLVTGLVNLELYKLIDNKTDIEQYKNGFVNLALPFFGFSEPIASPKGEYNNKKYDKIWDRFDIKGDIKLSDLIEHFEKDEGLEITMLSYGVSLLYASFFPPKKLKERLNLPITQLVKLVTKKDIPAHVSTMILEICADDKEGEDVEVPFITIHL

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ubiquitin
Molecular weight formula_weight	8568.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;Baker's yeast ;
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PROLINE
Molecular weight formula_weight	115.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cmmb_
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	d3cmmd_
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

CATH v4.4 (14 domains)

Domain ID domain_id	3cmmA01
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	3cmmA02
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	3cmmA03
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	3cmmA04
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	3cmmA05
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	3cmmA06
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	3cmmB00
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	3cmmC01
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	3cmmC02
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	3cmmC03
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	3cmmC04
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	3cmmC05
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	3cmmC06
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	3cmmD00
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

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8. Citations (1)

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Unit-cell length a length_a	115.363 Å
Unit-cell length b length_b	118.564 Å
Unit-cell length c length_c	207.567 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1936
R_work r_work	0.1908
R_free r_free	0.2469

fit	/app/data/saxs_computation/cm/3cmm/3cmm.fit
pddf	/app/data/pr_computation/cm/3cmm/3cmm.pr.out
profile	/app/data/saxs_computation/cm/3cmm/3cmm.dat

Crystal Structure of the Uba1-Ubiquitin Complex

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (2 domains)

CATH v4.4 (14 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)