SAXSdb — 3h8v

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

Ubiquitin-like modifier-activating enzyme 5

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	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 57–329 Chain B； UniProt 57–329	Fragment：residues 57-329	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

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 3H8V	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 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
5IAA Crystal structure of human UBA5 in complex with UFM1 Deposited 2016-02-21	Different construct 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 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
7NVK Crystal structure of UBA5 fragment fused to the N-terminus of UFC1 Deposited 2021-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 347–404（58 aa）	Not recorded	No recorded non-water small molecule	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
7NW1 Crystal structure of UFC1 in complex with UBA5 Deposited 2021-03-16	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 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 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 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 mutation/modification Different oligomeric state 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 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 A； PDBConstruct 20–292； UniProt 57–329 Author chain B； PDBConstruct 20–292； UniProt 57–329

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3h8v
Deposition date deposition_date	2009-04-29
Structure title title	Human Ubiquitin-activating Enzyme 5 in Complex with ATP
Keywords keywords	ROSSMANN FOLD, ATP-BINDING, UBL CONJUGATION PATHWAY, TRANSFERASE, STRUCTURAL GENOMICS CONSORTIUM, SGC; 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	24.99 Å
Radius of gyration Rg (electron density) rg_electron	23.93 Å
Forward intensity I(0) i0	41776800.00
Molecular weight molecular_weight	49083.0 kDa
Excluded volume excluded_volume	61055 Å³
Envelope volume envelope_volume	73561 Å³
Hydration-shell volume shell_volume	26144 Å³
Envelope diameter envelope_diameter	82.6 Å
Shell Rg shell_rg	30.75 Å
Envelope Rg envelope_rg	24.14 Å
Shape Rg shape_rg	23.95 Å
Total Rg total_rg	24.66 Å
Total atoms total_atoms	3425
Residues n_residues	453
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	80.6 Å
Rg (real space) rg_real	25.06 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	4.1780e+07
I(0) uncertainty (real space) i0_real_error	6.0540e+05
Rg (reciprocal space) rg_reciprocal	25.04 Å
I(0) (reciprocal space) i0_reciprocal	41780000.0000
Solution quality estimate total_estimate	0.8874
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.428
Kurtosis Kurtosis kurtosis	-0.327
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4760000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.965

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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-like modifier-activating enzyme 5
Molecular weight formula_weight	32165.9 kDa
EC 编号 ec_number	2.7.7.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3615

MGSSHHHHHHSSGLVPRGSMALKRMGIVSDYEKIRTFAVAIVGVGGVGSVTAEMLTRCGIGKLLLFDYDKVELANMNRLFFQPHQAGLSKVQAAEHTLRNINPDVLFEVHNYNITTVENFQHFMDRISNGGLEEGKPVDLVLSCVDNFEARMTINTACNELGQTWMESGVSENAVSGHIQLIIPGESACFACAPPLVVAANIDEKTLKREGVCAASLPTTMGVVAGILVQNVLKFLLNFGTVSFYLGYNAMQDFFPTMSMKPNPQCDDRNCRKQQEEYKKKVAALPKQEVIQ

来源 Source

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3h8vA00
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	3h8vB00
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

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8. Citations (1)

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Unit-cell length a length_a	77.999 Å
Unit-cell length b length_b	77.999 Å
Unit-cell length c length_c	207.005 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.530 Å
R factor r_factor	0.1930
R_work r_work	0.1910
R_free r_free	0.2240

fit	/app/data/saxs_computation/h8/3h8v/3h8v.fit
pddf	/app/data/pr_computation/h8/3h8v/3h8v.pr.out
profile	/app/data/saxs_computation/h8/3h8v/3h8v.dat

Human Ubiquitin-activating Enzyme 5 in Complex with ATP

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

Ubiquitin-like modifier-activating enzyme 5

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