SAXSdb — 1wzv

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

Ubiquitin-conjugating enzyme E2 L6

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 A； UniProt 1–152	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.10 Å R-free 0.267
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–152	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.10 Å R-free 0.267

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 1WZV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WZW Crystal Structure of UbcH8 Deposited 2005-03-10	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–152（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；PEG 3350, calcium acetate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.274
2KJH NMR based structural model of the UBCH8-UBIQUITIN complex Deposited 2009-05-28	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 1–152（152 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 250；Pressure ambient NMR sample composition 0.35 mM [U-100% 13C; U-100% 15N] UbcH8-1, 0.35 mM Ubiquitin-2, 20 mM sodium phosphate-3, 1 mM EDTA-4, 250 mM sodium chloride-5, 50 mM Arginine-6, 50 mM Glutamic Acid-7, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM UbcH8-8, 0.35 mM [U-100% 13C; U-100% 15N] Ubiquitin-9, 20 mM sodium phosphate-10, 1 mM EDTA-11, 250 mM sodium chloride-12, 50 mM Arginine-13, 50 mM Glutamic Acid-14, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM [U-100% 15N; U-99% 2H] UbcH8-15, 0.35 mM Ubiquitin-16, 20 mM sodium phosphate-17, 1 mM EDTA-18, 250 mM sodium chloride-19, 50 mM Arginine-20, 50 mM Glutamic Acid-21, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.35 mM UbcH8-22, 0.35 mM [U-100% 15N; U-99% 2H] Ubiquitin-23, 20 mM sodium phosphate-24, 1 mM EDTA-25, 250 mM sodium chloride-26, 50 mM Arginine-27, 50 mM Glutamic Acid-28, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8OIF Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6 Deposited 2023-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 1–153（153 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8SE9 Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 2) Deposited 2023-04-08	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 × 4 PDB declaration: tetrameric	Chain C 2–153（152 aa）	Mutation：C98S,C102S,L121K	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8SEA Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex (Form 1) Deposited 2023-04-08	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 × 4 PDB declaration: tetrameric	Chain C 2–153（152 aa）	Mutation：C98S,C102S,L121K	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8SEB Cryo-EM structure of a single loaded human UBA7-UBE2L6-ISG15 adenylate complex Deposited 2023-04-08	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 × 3 PDB declaration: trimeric	Chain C 2–153（152 aa）	Mutation：C98S,C102S,L121K	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8SV8 Cryo-EM structure of a double loaded human UBA7-UBE2L6-ISG15 thioester mimetic complex from a composite map Deposited 2023-05-15	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 × 4 PDB declaration: tetrameric	Chain C 2–153（152 aa）	Mutation：C98S/C102S/L121K	AMP ADENOSINE MONOPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.38 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UBC8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–155； UniProt 1–152 Author chain B； PDBConstruct 4–155； UniProt 1–152

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	1wzv
Deposition date deposition_date	2005-03-10
Structure title title	Crystal Structure of UbcH8
Keywords keywords	UBIQUITIN, UBIQUITIN CONJUGATING ENZYME, E2, 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	24.78 Å
Radius of gyration Rg (electron density) rg_electron	23.93 Å
Forward intensity I(0) i0	19507400.00
Molecular weight molecular_weight	34807.0 kDa
Excluded volume excluded_volume	44153 Å³
Envelope volume envelope_volume	54993 Å³
Hydration-shell volume shell_volume	19830 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	29.89 Å
Envelope Rg envelope_rg	23.85 Å
Shape Rg shape_rg	23.86 Å
Total Rg total_rg	24.96 Å
Total atoms total_atoms	2454
Residues n_residues	300
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	87.4 Å
Rg (real space) rg_real	24.81 Å
Rg uncertainty (real space) rg_real_error	0.99 Å
I(0) (real space) i0_real	1.9510e+07
I(0) uncertainty (real space) i0_real_error	3.0330e+05
Rg (reciprocal space) rg_reciprocal	24.81 Å
I(0) (reciprocal space) i0_reciprocal	19510000.0000
Solution quality estimate total_estimate	0.7528
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.298
Kurtosis Kurtosis kurtosis	-0.584
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4939000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 0.971; Sysdev: 1.000; Positv: 1.000; Valcen: 0.767; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1wzva1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.1 — UBC-related

Domain ID domain_id	d1wzva2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1wzvb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.20 — UBC-like
Superfamily Superfamily superfamily	d.20.1 — UBC-like
Family Family family	d.20.1.0 — automated matches

Domain ID domain_id	d1wzvb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1wzvA00
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	1wzvB00
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	54.231 Å
Unit-cell length b length_b	35.486 Å
Unit-cell length c length_c	92.580 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.55 °
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	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2095
R_work r_work	0.2066
R_free r_free	0.2673

Description description	Ubiquitin-conjugating enzyme E2 L6
Molecular weight formula_weight	17941.8 kDa
EC 编号 ec_number	6.3.2.19
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2592

Crystal Structure of UbcH8

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

Ubiquitin-conjugating enzyme E2 L6

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

fit	/app/data/saxs_computation/wz/1wzv/1wzv.fit
pddf	/app/data/pr_computation/wz/1wzv/1wzv.pr.out
profile	/app/data/saxs_computation/wz/1wzv/1wzv.dat