MolNFT v1 · #17776 · protein
Mechanism of ubiquitin recognition by the cue domain of VPS9
1P3Q · Vacuolar protein sorting-associated protein VPS9: “Mechanism of ubiquitin recognition by the cue domain of VPS9”. X-ray diffraction, 3 pockets (best druggability 0.58). MolNFT v1 #17776 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1P3Q
- Type
- protein
- Length
- 228 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein VPS9; Ubiquitin
- UniProt
- P54787, P62990
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | Vacuolar protein sorting-associated protein VPS9 | protein | 45 | 71% helix, 0% strand | P54787 |
| R | Vacuolar protein sorting-associated protein VPS9 | protein | 36 | 58% helix, 0% strand | P54787 |
| U | Ubiquitin | protein | 74 | 24% helix, 35% strand | P62990 |
| V | Ubiquitin | protein | 73 | 25% helix, 34% strand | P62990 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.58 | 0.79 | 34 | empty |
| 2 | 109 | 0.45 | 0.78 | 18 | empty |
| 3 | 115 | 0.37 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- Q–R · 731 Ų buried · 1 hydrogen bond · protein-protein
- R–V · 493 Ų buried · 4 hydrogen bonds · protein-protein
- U–V · 384 Ų buried · 7 hydrogen bonds · protein-protein
- Q–V · 279 Ų buried · 1 hydrogen bond · protein-protein
- Q–U · 135 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 1P3Q · Mechanism of Ubiquitin Recognition by the CUE Domain of VPS9 · the same entry in another collection · chain Q against Q, TM-score 1.00
- P54787 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 9… · a predicted model of the same protein · chain Q against A, TM-score 0.69
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 P54787
- Every structure of UniProt P62990
- Elsewhere: RCSB PDB 1P3Q · PDBe 1P3Q · UniProt P54787 · UniProt P62990
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