MolNFT v1 · #191244 · protein
X-ray structure of the WD40 domain of hops subunit VPS11 from yeast
8CUK · E3 ubiquitin-protein ligase PEP5: “X-ray structure of the WD40 domain of hops subunit VPS11 from yeast”. X-ray diffraction, 9 pockets (best druggability 0.78). MolNFT v1 #191244 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8CUK
- Type
- protein
- Length
- 994 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase PEP5
- EC
- 2.3.2.27
- UniProt
- P12868
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase PEP5 (EC 2.3.2.27) | protein | 330 | 2% helix, 54% strand | P12868 |
| B | E3 ubiquitin-protein ligase PEP5 (EC 2.3.2.27) | protein | 334 | 3% helix, 55% strand | P12868 |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.78 | 0.81 | 64 | empty |
| 2 | 950 | 0.78 | 0.80 | 80 | empty |
| 3 | 812 | 0.76 | 0.80 | 57 | empty |
| 4 | 83 | 0.58 | 0.88 | 23 | empty |
| 5 | 97 | 0.47 | 0.81 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 828 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 783 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 8CUK · X-ray Structure of the WD40 domain of HOPS subunit Vps11 from Yeast · the same entry in another collection · chain A against A, TM-score 1.00
- P12868 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase PEP5 (P12868) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P12868
- Elsewhere: RCSB PDB 8CUK · PDBe 8CUK · UniProt P12868
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