MolNFT v1 · #190425 · protein
Crystal structure of VPS17P px from S. cerevisiae (space)
7X4O · Vacuolar protein sorting-associated protein 17: “Crystal structure of VPS17P px from S. cerevisiae (space)”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.73). MolNFT v1 #190425 on GenesisL1: 3D structure…
- PDB
- 7X4O
- Type
- protein
- Length
- 248 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacuolar protein sorting-associated protein 17
- UniProt
- P32913
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vacuolar protein sorting-associated protein 17 | protein | 120 | 42% helix, 20% strand | P32913 |
| B | Vacuolar protein sorting-associated protein 17 | protein | 128 | 40% helix, 20% strand | P32913 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 51 | 0.73 | 0.99 | 14 | empty |
| 2 | 80 | 0.37 | 0.77 | 16 | empty |
| 3 | 65 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 938 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7X4O · Crystal structure of Vps17p PX from S. cerevisiae (Space) · the same entry in another collection · chain A against A, TM-score 1.00
- P32913 · AlphaFold monomer V2.0 prediction for vacuolar protein sorting- associated protein 17… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P32913
- Elsewhere: RCSB PDB 7X4O · PDBe 7X4O · UniProt P32913
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