MolNFT v1 · #109956 · protein
Crystal structure of U-box 2 of lubx / LEGU2 / LPP2887 from legionella pneumophila str. paris, wild-type
4XI1 · E3 ubiquitin-protein ligase lubx: “Crystal structure of U-box 2 of lubx / LEGU2 / LPP2887 from legionella pneumophila str. paris, wild-type”. X-ray diffraction, 1 ligand (CL), 4 pockets (best druggability 0.63). MolNFT v1 #109956 on…
- PDB
- 4XI1
- Type
- protein
- Length
- 226 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase lubx
- EC
- 6.3.2.-
- UniProt
- Q5X159
- Ligands
- CL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase lubx (EC 6.3.2.-) | protein | 76 | 41% helix, 16% strand | Q5X159 |
| B | E3 ubiquitin-protein ligase lubx (EC 6.3.2.-) | protein | 75 | 43% helix, 16% strand | Q5X159 |
| C | E3 ubiquitin-protein ligase lubx (EC 6.3.2.-) | protein | 75 | 41% helix, 16% strand | Q5X159 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B, C
- HEZ · Hexane-1,6-diol · additive · 5 copies · chains A, B, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.63 | 0.80 | 23 | CL |
| 2 | 189 | 0.59 | 0.81 | 31 | HEZ |
| 3 | 91 | 0.42 | 0.78 | 14 | HEZ |
| 4 | 72 | 0.29 | 0.72 | 19 | HEZ |
Interfaces
3 interfaces between chains.
- A–B · 527 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 210 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4XI1 · Crystal structure of U-box 2 of LubX / LegU2 / Lpp2887 from Legionella pneumophila str.… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5X159 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase lubx (Q5X159) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q5X159
- Elsewhere: RCSB PDB 4XI1 · PDBe 4XI1 · UniProt Q5X159
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