MolNFT v1 · #146512 · protein
VPS1 GTPase-bse fusion complexed with GDP.ALF4-
6DJQ: “VPS1 GTPase-bse fusion complexed with GDP.ALF4-”. X-ray diffraction, 4 ligands (GDP, ALF, MG), 19 pockets (best druggability 0.84). MolNFT v1 #146512 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6DJQ
- Type
- protein
- Length
- 1,340 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VPS1 GTPase-bse
- UniProt
- G0SFF0
- Ligands
- GDP, ALF, MG, NA
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VPS1 GTPase-bse | protein | 340 | 44% helix, 14% strand | G0SFF0 |
| B | VPS1 GTPase-bse | protein | 330 | 47% helix, 15% strand | G0SFF0 |
| C | VPS1 GTPase-bse | protein | 343 | 47% helix, 14% strand | G0SFF0 |
| D | VPS1 GTPase-bse | protein | 327 | 42% helix, 15% strand | G0SFF0 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- ALF · Tetrafluoroaluminate ion · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.84 | 0.90 | 75 | GDP, ALF, MG, NA |
| 2 | 556 | 0.83 | 0.89 | 80 | GDP, ALF, MG, NA |
| 3 | 1123 | 0.83 | 0.84 | 75 | empty |
| 4 | 422 | 0.78 | 0.87 | 58 | GDP, ALF, MG, NA |
| 5 | 395 | 0.78 | 0.87 | 56 | GDP, ALF, MG, NA |
Interfaces
5 interfaces between chains.
- C–D · 1431 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1106 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 55 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DJQ · Vps1 GTPase-BSE fusion complexed with GDP.AlF4- · 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 G0SFF0
- Elsewhere: RCSB PDB 6DJQ · PDBe 6DJQ · UniProt G0SFF0
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