MolNFT v1 · #128648 · protein
Crystal structure of LINALOOL/NEROLIDOL synthase from streptomyces clavuligerus
5NX4 · Pentalenene synthase: “Crystal structure of LINALOOL/NEROLIDOL synthase from streptomyces clavuligerus”. X-ray diffraction, 9 pockets (best druggability 0.85). MolNFT v1 #128648 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5NX4
- Type
- protein
- Length
- 580 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
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentalenene synthase (EC 4.2.3.7) | protein | 293 | 75% helix, 0% strand | D5SL78 |
| B | Pentalenene synthase (EC 4.2.3.7) | protein | 287 | 75% helix, 0% strand | D5SL78 |
Ligands and binding sites
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.85 | 0.86 | 100 | empty |
| 2 | 458 | 0.77 | 0.85 | 48 | empty |
| 3 | 536 | 0.73 | 0.81 | 45 | empty |
| 4 | 122 | 0.49 | 0.80 | 25 | empty |
| 5 | 127 | 0.49 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1584 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5NX4 · Crystal structure of Linalool/Nerolidol synthase from Streptomyces clavuligerus · 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 5NX4 · PDBe 5NX4 · UniProt D5SL78
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