SAXSdb — 7ahf

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

Ubiquitin-conjugating enzyme E2 S

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 1–156 Chain B； UniProt 1–156	Not recorded	EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M magnesium formate dihydrate, 15% PEG 3350	Resolution 2.15 Å R-free 0.239

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 7AHF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZDN Ubiquitin-conjugating enzyme E2S Deposited 2005-04-14	Different construct 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 1–156（156 aa） Fragment：N-terminal domain, residues 1-156	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；3M Na formate, 0.1M bisTris, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.93 Å R-free 0.234
1ZDN Ubiquitin-conjugating enzyme E2S Deposited 2005-04-14	Different construct 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 1–156（156 aa） Fragment：N-terminal domain, residues 1-156	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；3M Na formate, 0.1M bisTris, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.93 Å R-free 0.234
1ZDN Ubiquitin-conjugating enzyme E2S Deposited 2005-04-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–156（156 aa） Fragment：N-terminal domain, residues 1-156 Chain B 1–156（156 aa） Fragment：N-terminal domain, residues 1-156	Not recorded	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；3M Na formate, 0.1M bisTris, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.93 Å R-free 0.234
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–156（156 aa）	Mutation：C118M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000	Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–156（156 aa）	Mutation：C118M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000	Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–156（156 aa）	Mutation：C118M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000	Resolution 2.49 Å R-free 0.304
5BNB Crystal structure of a Ube2S-ubiquitin conjugate Deposited 2015-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–156（156 aa）	Mutation：C118M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1M Tris, 20% PEG 4000	Resolution 2.49 Å R-free 0.304
5L9T Model of human Anaphase-promoting complex/Cyclosome (APC/C-CDH1) with E2 UBE2S poised for polyubiquitination where UBE2S, APC2, and APC11 are modeled into low resolution density Deposited 2016-06-11	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 × 22 PDB declaration: 22-meric	Chain T 1–222（222 aa）	Mutation：C118F, delta 161-201	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.40 Å
6QH3 Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M Deposited 2019-01-15	Different construct 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 B 1–156（156 aa）	Mutation：C118M	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M magnesium chloride, 0.1 M hepes pH 7.5, 25% PEG 3350	Resolution 2.90 Å R-free 0.230
6QH3 Catalytic domain of the human ubiquitin-conjugating enzyme UBE2S C118M Deposited 2019-01-15	Different construct 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 A 1–156（156 aa）	Mutation：C118M	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2 M magnesium chloride, 0.1 M hepes pH 7.5, 25% PEG 3350	Resolution 2.90 Å R-free 0.230
6QHK PAO-linked dimer of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S Deposited 2019-01-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–156（156 aa） Chain B 1–156（156 aa）	Not recorded	CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 3 PA0 Phenylarsine oxide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；1 mM TCEP, 11.74 mg/ml PAO, 0.2 M magnesium chloride, 0.1 M Tris pH 8.5, 30% PEG 4000	Resolution 1.96 Å R-free 0.223
6S96 Crystal structure of the catalytic domain of UBE2S C118A. Deposited 2019-07-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–156（156 aa） Chain B 1–156（156 aa）	Not recorded	FMT FORMIC ACID × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293.15 K；2.5 M potassium formate, 0.1 M sodium cacodylate	Resolution 2.18 Å R-free 0.246
6S98 Crystal structure of the catalytic domain of UBE2S WT. Deposited 2019-07-11	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–156（156 aa） Chain B 1–156（156 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；293 K；0.2 M sodium-acetate-trihydrate; 0.1 M Tris; 30% PEG4000	Resolution 1.55 Å R-free 0.184
8TAU APC/C-CDH1-UBE2C-UBE2S-Ubiquitin-CyclinB Deposited 2023-06-27	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 × 23 PDB declaration: 23-meric	Chain E 205–222（18 aa） Fragment：C-terminal 18 residues	Not recorded	ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

8 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBE2S_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 1–156 Author chain B； PDBConstruct 1–156； UniProt 1–156

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	7ahf
Deposition date deposition_date	2020-09-24
Structure title title	Dimeric structure of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S L114E varaiant
Keywords keywords	E2, UBE2S, dimer, cell cycle, TRANSFERASE; 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	20.52 Å
Radius of gyration Rg (electron density) rg_electron	19.54 Å
Forward intensity I(0) i0	18047100.00
Molecular weight molecular_weight	33407.0 kDa
Excluded volume excluded_volume	42399 Å³
Envelope volume envelope_volume	49999 Å³
Hydration-shell volume shell_volume	21313 Å³
Envelope diameter envelope_diameter	69.6 Å
Shell Rg shell_rg	26.06 Å
Envelope Rg envelope_rg	19.73 Å
Shape Rg shape_rg	19.54 Å
Total Rg total_rg	20.47 Å
Total atoms total_atoms	4497
Residues n_residues	297
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	66.5 Å
Rg (real space) rg_real	20.40 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.8050e+07
I(0) uncertainty (real space) i0_real_error	2.1360e+05
Rg (reciprocal space) rg_reciprocal	20.42 Å
I(0) (reciprocal space) i0_reciprocal	18050000.0000
Solution quality estimate total_estimate	0.8079
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.178
Kurtosis Kurtosis kurtosis	-0.369
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5154000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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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-conjugating enzyme E2 S
Molecular weight formula_weight	17404.9 kDa
EC 编号 ec_number	2.3.2.23
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	4632

MNSNVENLPPHIIRLVYKEVTTLTADPPDGIKVFPNEEDLTDLQVTIEGPEGTPYAGGLFRMKLLLGKDFPASPPKGYFLTKIFHPNVGANGEICVNVLKRDWTAELGIRHVLETIKCLLIHPNPESALNEEAGRLLLENYEEYAARARLLTEIHG

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

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
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	78

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	7ahfA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

Domain ID domain_id	7ahfB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	110 — Ubiquitin Conjugating Enzyme
Homologous superfamily homologous superfamily	10 — Ubiquitin Conjugating Enzyme

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8. Citations (1)

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Unit-cell length a length_a	45.317 Å
Unit-cell length b length_b	48.411 Å
Unit-cell length c length_c	70.127 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	43.320 Å
R factor r_factor	0.1936
R_work r_work	0.1911
R_free r_free	0.2390

fit	/app/data/saxs_computation/ah/7ahf/7ahf.fit
pddf	/app/data/pr_computation/ah/7ahf/7ahf.pr.out
profile	/app/data/saxs_computation/ah/7ahf/7ahf.dat

Dimeric structure of the catalytic domain of the human ubiquitin-conjugating enzyme UBE2S L114E varaiant

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

Ubiquitin-conjugating enzyme E2 S

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