Research workbench
Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2
Analyse Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WZ3
- Type
- protein
- Length
- 331 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens; Legionella pneumophila
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; E3 ubiquitin-protein ligase LubX
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P62837, Q5X159
- Pockets
- 2 · best druggability 0.48
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 148 | 34% helix, 17% strand | P62837 |
| B | E3 ubiquitin-protein ligase LubX (EC 6.3.2.-) | protein | 183 | 42% helix, 14% strand | Q5X159 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.48 | 0.75 | 36 | empty |
| 2 | 116 | 0.39 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 651 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (engineered).
Compared structures
- 4WZ3 · Crystal structure of the complex between LUBX/LEGU2/LPP2887 U-box 1 and homo sapiens… · the same entry in another collection · chain A against A, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q5X159 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase lubx (Q5X159) · a predicted model of the same protein · chain B against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P62837
- Every structure of UniProt Q5X159
- Elsewhere: RCSB PDB 4WZ3 · PDBe 4WZ3 · UniProt P62837 · UniProt Q5X159
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