SAXSdb — 9qii

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

Ubiquitin-like modifier-activating enzyme 6

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–1052	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.99 Å

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 9QII	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7PVN Crystal Structure of Human UBA6 in Complex with ATP Deposited 2021-10-05	Different mutation/modification 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 1–1052（1052 aa）	Mutation：C625A Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 4 MG MAGNESIUM ION × 1 CA CALCIUM ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Na-cacodylate, 0.16 M Ca-acetate, 15% PEG 8000 and 16% Glycerol	Resolution 2.71 Å R-free 0.262
7PVN Crystal Structure of Human UBA6 in Complex with ATP Deposited 2021-10-05	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–1052（1052 aa）	Mutation：C625A Non-standard monomer：Yes (specific site not provided by mmCIF)	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 4 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Na-cacodylate, 0.16 M Ca-acetate, 15% PEG 8000 and 16% Glycerol	Resolution 2.71 Å R-free 0.262
7PYV Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10 Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–623（623 aa） Chain A 900–1052（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；277 K；0.5 M Lithium chloride, 0.1 M Tris pH 8.4, 25% PEG 6000	Resolution 3.27 Å R-free 0.239
7PYV Crystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10 Deposited 2021-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–623（623 aa） Chain B 900–1052（153 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.4；277 K；0.5 M Lithium chloride, 0.1 M Tris pH 8.4, 25% PEG 6000	Resolution 3.27 Å R-free 0.239
7SOL Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6 Deposited 2021-10-31	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 A 37–1052（1016 aa）	Mutation：C625A	IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20 % PEG 3350, 0.2 M NaF	Resolution 2.25 Å R-free 0.206
7SOL Crystal Structures of the bispecific ubiquitin/FAT10 activating enzyme, Uba6 Deposited 2021-10-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 37–1052（1016 aa）	Mutation：C625A	AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；20 % PEG 3350, 0.2 M NaF	Resolution 2.25 Å R-free 0.206
9QGW Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (singly loaded) Deposited 2025-03-14	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
9QH5 Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded) Deposited 2025-03-14	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9QHI Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 0) Deposited 2025-03-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.27 Å
9QIA Structure of UBA6-UbDha-BIRC6 trapped ternary complex (cluster 2) Deposited 2025-03-18	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.38 Å
9QIC Consensus structure of UBA6 Deposited 2025-03-17	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
9QIG Structure of UBA6 (cluster 2) Deposited 2025-03-17	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9QIM Consensus structure of UBA6-BIRC6 Deposited 2025-03-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å
9QIO Structure of UBA6-BIRC6 (cluster 0) Deposited 2025-03-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.22 Å
9QIP Structure of UBA6-BIRC6 (cluster 4) Deposited 2025-03-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.15 Å
9QIV Consensus structure of UBA6-BIRC6 (alternative conformation) Deposited 2025-03-17	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–1052（1052 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å

13 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBA6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 3–1054； UniProt 1–1052

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	9qii
Deposition date deposition_date	2025-03-17
Structure title title	Structure of UBA6 (cluster 3)
Keywords keywords	E1, Ligase, SIGNALING PROTEIN; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	34.49 Å
Radius of gyration Rg (electron density) rg_electron	33.82 Å
Forward intensity I(0) i0	200993000.00
Molecular weight molecular_weight	114880.0 kDa
Excluded volume excluded_volume	144260 Å³
Envelope volume envelope_volume	189310 Å³
Hydration-shell volume shell_volume	46561 Å³
Envelope diameter envelope_diameter	113.6 Å
Shell Rg shell_rg	40.78 Å
Envelope Rg envelope_rg	33.31 Å
Shape Rg shape_rg	33.83 Å
Total Rg total_rg	34.33 Å
Total atoms total_atoms	8077
Residues n_residues	1011
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	109.6 Å
Rg (real space) rg_real	34.37 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	2.0100e+08
I(0) uncertainty (real space) i0_real_error	3.1060e+06
Rg (reciprocal space) rg_reciprocal	34.45 Å
I(0) (reciprocal space) i0_reciprocal	201000000.0000
Solution quality estimate total_estimate	0.9039
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.9 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	31070000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.922

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like modifier-activating enzyme 6
Molecular weight formula_weight	118250.8 kDa
EC 编号 ec_number	6.2.1.45
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	8077

GPMEGSEPVAAHQGEEASCSSWGTGSTNKNLPIMSTASVEIDDALYSRQRYVLGDTAMQKMAKSHVFLSGMGGLGLEIAKNLVLAGIKAVTIHDTEKCQAWDLGTNFFLSEDDVVNKRNRAEAVLKHIAELNPYVHVTSSSVPFNETTDLSFLDKYQCVVLTEMKLPLQKKINDFCRSQCPPIKFISADVHGIWSRLFCDFGDEFEVLDTTGEEPKEIFISNITQANPGIVTCLENHPHKLETGQFLTFREINGMTGLNGSIQQITVISPFSFSIGDTTELEPYLHGGIAVQVKTPKTVFFESLERQLKHPKCLIVDFSNPEAPLEIHTAMLALDQFQEKYSRKPNVGCQQDSEELLKLATSISETLEEKPDVNADIVHWLSWTAQGFLSPLAAAVGGVASQEVLKAVTGKFSPLCQWLYLEAADIVESLGKPECEEFLPRGDRYDALRACIGDTLCQKLQNLNIFLVGCGAIGCEMLKNFALLGVGTSKEKGMITVTDPDLIEKSNLNRQFLFRPHHIQKPKSYTAADATLKINSQIKIDAHLNKVCPTTETIYNDEFYTKQDVIITALDNVEARRYVDSRCLANLRPLLDSGTMGTKGHTEVIVPHLTESYNSHRDPPEEEIPFSTLKSFPAAIEHTIQWARDKFESSFSHKPSLFNKFWQTYSSAEEVLQKIQSGHSLEGCFQVIKLLSRRPRNWSQCVELARLKFEKYFNHKALQLLHCFPLDIRLKDGSLFWQSPKRPPSPIKFDLNEPLHLSFLQNAAKLYATVYCIPFAEEDLSADALLNILSEVKIQEFKPSNKVVQTDETARKPDHVPISSEDERNAIFQLEKAILSNEATKSDLQMAVLSFEKDDDHNGHIDFITAASNLRAKMYSIEPADRFKTKRIAGKIIPAIATTTATVSGLVALEMIKVTGGYPFEAYKNCFLNLAIPIVVFTETTEVRKTKIRNGISFTIWDRWTVHGKEDFTLLDFINAVKEKYGIEPTMVVQGVKMLYVPVMPGHAKRLKLTMHKLVKPTTEKKYVDLTVSFAPDIDGDEDLPGPPVRYYFSHDTD

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	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	1

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

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8. Citations (1)

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Resolution resolution	3.99 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	17392

fit	/app/data/saxs_computation/qi/9qii/9qii.fit
pddf	/app/data/pr_computation/qi/9qii/9qii.pr.out
profile	/app/data/saxs_computation/qi/9qii/9qii.dat

Structure of UBA6 (cluster 3)