MolNFT v1 · #82355 · protein
Crystal structure of MOEO5 soaked with fspp overnight
3VKB: “Crystal structure of MOEO5 soaked with fspp overnight”. X-ray diffraction, 4 ligands (POP, FPS, MG), 6 pockets (best druggability 0.75). MolNFT v1 #82355 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VKB
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MOEO5
- UniProt
- A0A011
- Ligands
- POP, FPS, MG, CL
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MOEO5 | protein | 253 | 40% helix, 19% strand | A0A011 |
| B | MOEO5 | protein | 254 | 41% helix, 19% strand | A0A011 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.75 | 0.87 | 36 | POP, FPS |
| 2 | 304 | 0.74 | 0.86 | 34 | POP, FPS |
| 3 | 128 | 0.55 | 0.82 | 24 | CL |
| 4 | 101 | 0.45 | 0.79 | 21 | empty |
| 5 | 87 | 0.40 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1188 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3VKB · Crystal structure of MoeO5 soaked with FsPP overnight · 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 A0A011
- Elsewhere: RCSB PDB 3VKB · PDBe 3VKB · UniProt A0A011
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