MolNFT v1 · #167393 · protein
The P-loop K to a mutation of C. therm VPS1 GTPase-bse
6VJF · Putative sorting protein VPS1: “The P-loop K to a mutation of C. therm VPS1 GTPase-bse”. X-ray diffraction, 2 ligands (GCP, MG), 16 pockets (best druggability 0.82). MolNFT v1 #167393 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6VJF
- Type
- protein
- Length
- 1,432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative sorting protein VPS1
- UniProt
- G0SFF0
- Ligands
- GCP, MG
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative sorting protein VPS1 | protein | 361 | 44% helix, 14% strand | G0SFF0 |
| B | Putative sorting protein VPS1 | protein | 358 | 46% helix, 14% strand | G0SFF0 |
| C | Putative sorting protein VPS1 | protein | 365 | 45% helix, 14% strand | G0SFF0 |
| D | Putative sorting protein VPS1 | protein | 348 | 44% helix, 15% strand | G0SFF0 |
Ligands and binding sites
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium 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
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.82 | 0.87 | 83 | GCP, MG |
| 2 | 690 | 0.79 | 0.84 | 85 | GCP, MG |
| 3 | 845 | 0.78 | 0.82 | 104 | GCP, MG |
| 4 | 1107 | 0.78 | 0.80 | 113 | empty |
| 5 | 632 | 0.77 | 0.83 | 81 | GCP, MG |
Interfaces
4 interfaces between chains.
- A–B · 1461 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1460 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 933 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 80 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6VJF · The P-Loop K to A mutation of C. therm Vps1 GTPase-BSE · 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 6VJF · PDBe 6VJF · UniProt G0SFF0
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