7nvk

Crystal structure of UBA5 fragment fused to the N-terminus of UFC1

Method: X-RAY DIFFRACTION D_max: 78.5 Å Quality: GOOD

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

Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain AAA； UniProt 347–404	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2% (v/v) Tacsimate pH 7.0, 20% PEG 3350, 0.1M HEPES pH 7.5, 6mM zinc sulfate	Resolution 2.65 Å R-free 0.264

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 7NVK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3GUC Human Ubiquitin-activating Enzyme 5 in Complex with AMPPNP Deposited 2009-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 57–329（273 aa） Chain B 57–329（273 aa）	Not recorded	ZN ZINC ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；287 K；1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE,0.1 M SODIUM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 287K	Resolution 2.25 Å R-free 0.255
3H8V Human Ubiquitin-activating Enzyme 5 in Complex with ATP Deposited 2009-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 57–329（273 aa） Fragment：residues 57-329 Chain B 57–329（273 aa） Fragment：residues 57-329	Not recorded	ZN ZINC ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；287 K；1 M LITHIUM SULPHATE, 0.3 M AMMONIUM SULPHATE, 0.1 M SODIUM CITRATE, PH 6.2 , VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.00 Å R-free 0.224
5IAA Crystal structure of human UBA5 in complex with UFM1 Deposited 2016-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 57–346（290 aa） Fragment：UNP residues 57-346 Chain B 57–346（290 aa） Fragment：UNP residues 57-346	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；8% Tascimate, pH 7.0 and 16% PEG3350	Resolution 1.85 Å R-free 0.206
5L95 Crystal structure of human UBA5 in complex with UFM1 and AMP Deposited 2016-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 68–346（279 aa） Chain B 68–346（279 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.1M HEPES pH7.5, 10% PEG 6000 and 5% 2-Methyl-2,4-pentanediol (MPD)	Resolution 2.10 Å R-free 0.222
6H77 E1 enzyme for ubiquitin like protein activation in complex with UBL Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 36–346（311 aa） Chain B 36–346（311 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 2.10 Å R-free 0.221
6H77 E1 enzyme for ubiquitin like protein activation in complex with UBL Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 36–346（311 aa） Chain D 36–346（311 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 17 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；293.15 K；0.2 M Lithium Nitrate, 21% PEG 3350, 0.2 M Magnesium chloride hexahydrate and 3.5 % v/v Pentaerythritol ethoxylate (3/4 EO/OH)	Resolution 2.10 Å R-free 0.221
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 36–335（300 aa） Chain B 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 36–335（300 aa） Chain D 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 36–335（300 aa） Chain F 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 36–335（300 aa） Chain H 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 36–335（300 aa） Chain J 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain K 36–335（300 aa） Chain L 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain M 36–335（300 aa） Chain N 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H78 E1 enzyme for ubiquitin like protein activation. Deposited 2018-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain O 36–335（300 aa） Chain P 36–335（300 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 4 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293.13 K；0.2M sodium citrate tribasic dihydrate pH 7.9, 20% PEG 3350.	Resolution 2.70 Å R-free 0.242
6H8C Structure of the human GABARAPL2 protein in complex with the UBA5 LIR motif Deposited 2018-08-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 333–348（16 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 0.6 mM [U-99% 13C; U-99% 15N] GABARAPL2, 1.0 mM No Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM No GABARAPL2, 0.6 mM [U-99% 13C; U-99% 15N] Ubiquitin-like modifier-activating enzyme 5 (UBA5) LIR motif, 50 mM No sodium phosphate, 100 mM No sodium chloride, 4.6 mM No sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	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 FFF 389–404（16 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride	Resolution 1.95 Å R-free 0.280
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	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 CCC 389–404（16 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride	Resolution 1.95 Å R-free 0.280
7OVC Structure of the human UFC1 protein in complex with the UBA5 C-terminal UFC1-binding motif. Deposited 2021-06-14	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 381–404（24 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] Ubiquitin-fold modifier-conjugating enzyme 1, 1.0 mM Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.2 mM Ubiquitin-fold modifier-conjugating enzyme 1, 0.3 mM [U-100% 13C; U-100% 15N] Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

9 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBA5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 2–59； UniProt 347–404

Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1

Homo sapiens

UniProt Q9Y3C8

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain AAA； UniProt 1–167	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2% (v/v) Tacsimate pH 7.0, 20% PEG 3350, 0.1M HEPES pH 7.5, 6mM zinc sulfate	Resolution 2.65 Å R-free 0.264

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7NVK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K07 Solution NMR structure of human E2-like ubiquitin-fold modifier conjugating enzyme 1 (UFC1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-01-25	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) na；Pressure ambient NMR sample composition 1.1 mM [U-100% 13C; U-100% 15N] protein UFC1, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2Z6O Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1 Deposited 2007-08-06	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 1–167（167 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；28% (w/v) PEG 4000, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.221
2Z6P Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1 Deposited 2007-08-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5M ammonium sulfate, 0.1M MES pH 7.0, 10%(w/v) dioxan, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.243
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
3EVX Crystal structure of the human E2-like ubiquitin-fold modifier conjugating enzyme 1 (Ufc1). Northeast Structural Genomics Consortium target HR41 Deposited 2008-10-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–167（167 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SCN THIOCYANATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291 K；Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution:100mM Sodium acetate, 18% PEG8000, 100mM (NH4)SCN, 50mM LiSCN, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.54 Å R-free 0.279
7NVJ Crystal structure of UFC1 Y110A & F121A Deposited 2021-03-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：Y110A, F121A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES pH 7.5, 2M Ammonium sulfate	Resolution 2.20 Å R-free 0.246
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain AAA 1–167（167 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 2 PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride	Resolution 1.95 Å R-free 0.280
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain BBB 1–167（167 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；35 mM citric acid, 65 mM bis-tris propane, 19% PEG3350, 100 mM lithium chloride	Resolution 1.95 Å R-free 0.280
7OVC Structure of the human UFC1 protein in complex with the UBA5 C-terminal UFC1-binding motif. Deposited 2021-06-14	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–167（167 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure AMBIENT NMR sample composition 1.0 mM [U-100% 13C; U-100% 15N] Ubiquitin-fold modifier-conjugating enzyme 1, 1.0 mM Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.2 mM Ubiquitin-fold modifier-conjugating enzyme 1, 0.3 mM [U-100% 13C; U-100% 15N] Ubiquitin-like modifier-activating enzyme 5, 50 mM TRIS, 100 mM sodium chloride, 2 mM TCEP, 5 mM AEBSF protease inhibitor, 0.15 mM DSS, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
8BZR UFC1-UFM1 conjugate Deposited 2022-12-15	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 1–167（167 aa）	Mutation：C116K	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；30% v/v PEG400, 0.1M Tris, 0.2M Na citrate	Resolution 1.78 Å R-free 0.226
8C0D UFL1/DDRGK1 bound to UFC1 Deposited 2022-12-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
8C0D UFL1/DDRGK1 bound to UFC1 Deposited 2022-12-16	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–167（167 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；292 K；0.1M HEPES, 1.03M Li2SO4	Resolution 2.56 Å R-free 0.286
9GLH Crystal Structure of UFC1 T106S Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106S	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.4M Sodium Malonate dibasic monohydrate pH 6.0.	Resolution 1.11 Å R-free 0.192
9GLI Crystal Structure of UFC1 T106C Deposited 2024-08-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M Ammonium Citrate tribasic pH 7.0, 0.1M Bis-Tris Propane pH 7.0.	Resolution 1.43 Å R-free 0.208
9GLJ Crystal Structure of UFC1 T106A Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M NaCl, 0.1M Bis-Tris pH 6.5, 1.5M Ammonium sulfate.	Resolution 1.21 Å R-free 0.199
9GLK Crystal Structure of UFC1 E149I Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：E149I	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1M Bis-Tris pH 5.5, 2.0M Ammonium sulfate	Resolution 2.03 Å R-free 0.247
9GLL Crystal Structure of UFC1 T106L Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；1.4M Sodium potassium monobasic monohydrate/Potassium phosphate dibasic pH 9.0	Resolution 1.65 Å R-free 0.231
9GLM Crystal Structure of UFC1 W145F Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：W145F	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5M Ammonium sulfate; 0.1M Bis-Tris propane pH 7.0	Resolution 1.79 Å R-free 0.238
9GLN Crystal Structure of UFC1 C116E Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 1.8 M smmonium sulfate.	Resolution 1.92 Å R-free 0.227
9GLO Crystal Structure of UFC1 C116E&T106S Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E, T106S	GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate	Resolution 1.53 Å R-free 0.208
9GLP Crystal Structure of UFC1 C116E&T106I Deposited 2024-08-27	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E, T106I	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-Tris, pH 5.5, 2 M ammonium sulfate.	Resolution 1.77 Å R-free 0.200
9GMM Crystal Structure of UFC1 T106I Deposited 2024-08-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106I	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.5M Ammonium sulfate, 0.1M Bis-Tris Propane pH 7.0	Resolution 1.35 Å R-free 0.201
9GMN Crystal Structure of UFC1 T106V Deposited 2024-08-29	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：T106V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5M Ammonium sulfate, 0.1M Tris pH 8.0.	Resolution 2.00 Å R-free 0.231
9GN8 Crystal Structure of UFC1 E149D Deposited 2024-08-31	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：E149D	EDO 1,2-ETHANEDIOL × 1 FMT FORMIC ACID × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；2% (v/v) Tacsimate Ph 7.0, 0.1M Hepes pH 7.5, 20% (w/v) PEG 3350	Resolution 1.96 Å R-free 0.257
9I9M Crystal structure of chimeric UFC1, TAK MotiF replaced with HPN motif of other E2 proteins Deposited 2025-02-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1M sodium citrate tribasic dihydrate pH 5.5, 20% w/v 2-propanol, 20% w/v PEG 4000	Resolution 1.54 Å R-free 0.209
9I9N Crystal Structure of UFC1 C116E & K108A Deposited 2025-02-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：C116E, K108A	GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M Tris pH 8.0, 2M Ammonium sulfate	Resolution 1.88 Å R-free 0.229
9I9O Crystal Structure of UFC1 K108M Deposited 2025-02-06	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：K108M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.15M Ammonium sulfate, 0.1M Sodium Hepes pH 7.0, 20%w/v PEG 4000	Resolution 2.05 Å R-free 0.253
9I9P Crystal Structure of UFC1 W145H Deposited 2025-02-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：W145H	GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M Lithium sulfate monohydrate, 0.1M HEPES pH 7.5, 25% w/v PEG 3350	Resolution 2.02 Å R-free 0.267
9IA8 Crystal Structure of UFC1 K108R Deposited 2025-02-08	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 1–167（167 aa）	Mutation：K08R	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.1M Bis-Tris pH 5.5, 2M Ammonium Sulfate	Resolution 1.90 Å R-free 0.247

26 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UFC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain AAA； PDBConstruct 60–226； UniProt 1–167

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	7nvk
Deposition date deposition_date	2021-03-15
Structure title title	Crystal structure of UBA5 fragment fused to the N-terminus of UFC1
Keywords keywords	;Ubiquitin like fold modifier enzyme 5 (UBA5), E1, Ubiquitin fold modifier 1 (UFM1), Ubiquitin fold modifier conjugating enzyme 1 (UFC1), UFMYLATION, LIGASE ;; LIGASE
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	20.72 Å
Radius of gyration Rg (electron density) rg_electron	19.93 Å
Forward intensity I(0) i0	8024160.00
Molecular weight molecular_weight	21121.0 kDa
Excluded volume excluded_volume	26641 Å³
Envelope volume envelope_volume	33931 Å³
Hydration-shell volume shell_volume	15610 Å³
Envelope diameter envelope_diameter	79.2 Å
Shell Rg shell_rg	24.35 Å
Envelope Rg envelope_rg	21.49 Å
Shape Rg shape_rg	19.85 Å
Total Rg total_rg	20.95 Å
Total atoms total_atoms	1488
Residues n_residues	183
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	78.5 Å
Rg (real space) rg_real	20.93 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	8.0240e+06
I(0) uncertainty (real space) i0_real_error	1.1360e+05
Rg (reciprocal space) rg_reciprocal	20.89 Å
I(0) (reciprocal space) i0_reciprocal	8024000.0000
Solution quality estimate total_estimate	0.7755
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.7 Å
Skewness Skewness skewness	0.667
Kurtosis Kurtosis kurtosis	0.190
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1252000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.468; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.679; Smooth: 0.993

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	84.630 Å
Unit-cell length b length_b	84.630 Å
Unit-cell length c length_c	60.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.651 Å
Low-resolution limit resolution_low	46.780 Å
R factor r_factor	—
R_work r_work	0.2165
R_free r_free	0.2638

Description description	Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1
Molecular weight formula_weight	25917.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	AAA
Atom count atom_count	1488

Crystal structure of UBA5 fragment fused to the N-terminus of UFC1

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

Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like modifier-activating enzyme 5,Ubiquitin-fold modifier-conjugating enzyme 1

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/nv/7nvk/7nvk.fit
pddf	/app/data/pr_computation/nv/7nvk/7nvk.pr.out
profile	/app/data/saxs_computation/nv/7nvk/7nvk.dat