Research workbench
Structural identification of the VPS18 beta-propeller reveals a critical role in the hops complex stability and function.
Analyse Structural identification of the VPS18 beta-propeller reveals a critical role… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UUY
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar membrane protein PEP3
- UniProt
- P27801
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar membrane protein PEP3 | protein | 317 | 5% helix, 51% strand | P27801 |
| B | Vacuolar membrane protein PEP3 | protein | 318 | 6% helix, 51% strand | P27801 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · 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 | 1145 | 0.86 | 0.86 | 112 | SO4 |
| 2 | 647 | 0.74 | 0.80 | 92 | SO4 |
| 3 | 98 | 0.42 | 0.78 | 20 | empty |
| 4 | 59 | 0.37 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1447 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4UUY · Structural Identification of the Vps18 beta-propeller reveals a critical role in the HOPS… · the same entry in another collection · chain A against A, TM-score 1.00
- P27801 · AlphaFold monomer V2.0 prediction for vacuolar membrane protein PEP3 (P27801) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P27801
- Elsewhere: RCSB PDB 4UUY · PDBe 4UUY · UniProt P27801
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