Research workbench
VPS1 GTPase-bse fusion complexed with gmppcp
Analyse VPS1 GTPase-bse fusion complexed with gmppcp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DEF
- Type
- protein
- Length
- 1,429 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VPS1 GTPase-bse
- EC
- 3.-.-.-
- UniProt
- G0SFF0
- Ligands
- GCP, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VPS1 GTPase-bse (EC 3.-.-.-) | protein | 367 | 44% helix, 13% strand | G0SFF0 |
| B | VPS1 GTPase-bse (EC 3.-.-.-) | protein | 358 | 44% helix, 14% strand | G0SFF0 |
| C | VPS1 GTPase-bse (EC 3.-.-.-) | protein | 368 | 45% helix, 14% strand | G0SFF0 |
| D | VPS1 GTPase-bse (EC 3.-.-.-) | protein | 336 | 41% 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
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 824 | 0.81 | 0.84 | 106 | GCP, MG |
| 2 | 122 | 0.78 | 0.97 | 33 | empty |
| 3 | 465 | 0.77 | 0.86 | 60 | GCP, MG |
| 4 | 694 | 0.77 | 0.82 | 85 | GCP, MG |
| 5 | 638 | 0.77 | 0.83 | 77 | GCP, MG |
Interfaces
4 interfaces between chains.
- C–D · 1418 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1417 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 788 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 84 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DEF · Vps1 GTPase-BSE fusion complexed with GMPPCP · 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 6DEF · PDBe 6DEF · UniProt G0SFF0
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