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Crystal structure of LINALOOL/NEROLIDOL synthase from streptomyces clavuligerus in complex with 2-fluorogeranyl diphosphate
Analyse Crystal structure of LINALOOL/NEROLIDOL synthase from streptomyces clavuligerus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NX5
- Type
- protein
- Length
- 579 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentalenene synthase
- EC
- 4.2.3.7
- UniProt
- D5SL78
- Ligands
- 0FV, MG, CL, PO4
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentalenene synthase (EC 4.2.3.7) | protein | 287 | 79% helix, 0% strand | D5SL78 |
| B | Pentalenene synthase (EC 4.2.3.7) | protein | 292 | 76% helix, 0% strand | D5SL78 |
Ligands and binding sites
- 0FV · (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.83 | 0.84 | 104 | GOL |
| 2 | 432 | 0.80 | 0.88 | 45 | PO4 |
| 3 | 404 | 0.74 | 0.84 | 49 | MG, 0FV |
| 4 | 97 | 0.45 | 0.79 | 14 | empty |
| 5 | 77 | 0.42 | 0.80 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1638 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5NX5 · Crystal structure of Linalool/Nerolidol synthase from Streptomyces clavuligerus in… · the same entry in another collection · chain A against A, TM-score 1.00
- D5SL78 · AlphaFold monomer V2.0 prediction for R-linalool synthase (D5SL78) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 D5SL78
- Elsewhere: RCSB PDB 5NX5 · PDBe 5NX5 · UniProt D5SL78
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