MolNFT v1 · #189421 · protein
Crystal structure of VPS75 from candida albicans
7VF4: “Crystal structure of VPS75 from candida albicans”. X-ray diffraction, 2 ligands (NA, CL), 20 pockets (best druggability 0.82). MolNFT v1 #189421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VF4
- Type
- protein
- Length
- 1,750 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VPS75
- UniProt
- A0A1D8PT39
- Ligands
- NA, CL
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VPS75 | protein | 221 | 52% helix, 14% strand | A0A1D8PT39 |
| B | VPS75 | protein | 219 | 51% helix, 13% strand | A0A1D8PT39 |
| C | VPS75 | protein | 222 | 55% helix, 14% strand | A0A1D8PT39 |
| D | VPS75 | protein | 216 | 53% helix, 14% strand | A0A1D8PT39 |
| E | VPS75 | protein | 220 | 52% helix, 14% strand | A0A1D8PT39 |
| F | VPS75 | protein | 219 | 53% helix, 14% strand | A0A1D8PT39 |
| G | VPS75 | protein | 219 | 53% helix, 14% strand | A0A1D8PT39 |
| H | VPS75 | protein | 214 | 54% helix, 14% strand | A0A1D8PT39 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains B, A, C, D, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 965 | 0.82 | 0.84 | 106 | empty |
| 2 | 991 | 0.82 | 0.83 | 106 | empty |
| 3 | 642 | 0.76 | 0.82 | 71 | empty |
| 4 | 594 | 0.72 | 0.80 | 53 | empty |
| 5 | 472 | 0.66 | 0.78 | 46 | empty |
Interfaces
18 interfaces between chains.
- A–B · 1527 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 1523 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1505 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1431 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 932 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7VF4 · Crystal structure of Vps75 from Candida albicans · the same entry in another collection · 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 A0A1D8PT39
- Elsewhere: RCSB PDB 7VF4 · PDBe 7VF4 · UniProt A0A1D8PT39
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