9olb

Identification of ligands for E3 ligases using fragment-based methods

Method: X-RAY DIFFRACTION Dmax: 82.1 Å Quality: EXCELLENT

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

TNF receptor-associated factor 4

Homo sapiens

UniProt Q9BUZ4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 292–466 Not recorded Epidermal growth factor receptor × 1 (P00533) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5 Resolution 2.62 Å R-free 0.276
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 292–466 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5 Resolution 2.62 Å R-free 0.276
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 292–466 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5 Resolution 2.62 Å R-free 0.276

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.

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

View Construct and Data Evidence
UniProt name TRAF4_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–176; UniProt 292–466 Author chain B; PDBConstruct 2–176; UniProt 292–466 Author chain C; PDBConstruct 2–176; UniProt 292–466

Epidermal growth factor receptor

OrganismNot specified

UniProt P00533

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 1198–1207 Not recorded TNF receptor-associated factor 4 × 1 (Q9BUZ4) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;10-15% PEG 3350, 0.1 M Bis-TRIS pH 6.5 Resolution 2.62 Å R-free 0.276

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.

383 other PDB entries and 565 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EGFR_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–10; UniProt 1198–1207

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

SAXS profile for 9olb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9olb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9olb
Deposition date deposition_date2025-05-12
Structure title titleIdentification of ligands for E3 ligases using fragment-based methods
Keywords keywords;small molecule, complex crystal structure, CBL-c, TKB (TYROSINE KINASE BINDING), REGULATOR OF EGFR MEDIATED SIGNAL TRANSDUCTION, LIGASE ;; LIGASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.16
Radius of gyration Rg (electron density) rg_electron25.96
Forward intensity I(0) i046561700.00
Molecular weight molecular_weight53035.0 kDa
Excluded volume excluded_volume66326 ų
Envelope volume envelope_volume84724 ų
Hydration-shell volume shell_volume27471 ų
Envelope diameter envelope_diameter83.2
Shell Rg shell_rg32.99
Envelope Rg envelope_rg25.71
Shape Rg shape_rg25.93
Total Rg total_rg26.86
Total atoms total_atoms3776
Residues n_residues502
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax82.1
Rg (real space) rg_real27.03
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real4.6560e+07
I(0) uncertainty (real space) i0_real_error6.6800e+05
Rg (reciprocal space) rg_reciprocal27.07
I(0) (reciprocal space) i0_reciprocal46560000.0000
Solution quality estimate total_estimate0.9173
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary35.4
Skewness Skewness skewness0.101
Kurtosis Kurtosis kurtosis-0.672
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5683000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.981; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)