Research workbench
Crystal structure of 1,8-cineole synthase from streptomyces clavuligerus in complex with 2-fluoroneryl diphosphate and 2- fluorogeranyl diphosphate
Analyse Crystal structure of 1,8-cineole synthase from streptomyces clavuligerus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NX7
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentalenene synthase
- EC
- 4.2.3.7
- UniProt
- B5GMG2
- Ligands
- 0FV, LA6, 9D2, NDS, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentalenene synthase (EC 4.2.3.7) | protein | 308 | 71% helix, 0% strand | B5GMG2 |
| B | Pentalenene synthase (EC 4.2.3.7) | protein | 307 | 71% helix, 0% strand | B5GMG2 |
Ligands and binding sites
- 0FV · (2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- LA6 · (2E)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- 9D2 · 2-ethyl-2-(hydroxymethyl)propane-1,3-diol · ligand · 2 copies · chains A, B
- NDS · Ethyl dimethyl ammonio propane sulfonate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.79 | 0.90 | 43 | 0FV, LA6, MG |
| 2 | 89 | 0.78 | 0.98 | 23 | empty |
| 3 | 313 | 0.77 | 0.88 | 44 | 0FV, LA6, MG |
| 4 | 102 | 0.39 | 0.76 | 18 | empty |
| 5 | 96 | 0.38 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1153 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5NX7 · Crystal structure of 1,8-cineole synthase from Streptomyces clavuligerus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- B5GMG2 · AlphaFold monomer V2.0 prediction for 1,8-cineole synthase (B5GMG2) · 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 B5GMG2
- Elsewhere: RCSB PDB 5NX7 · PDBe 5NX7 · UniProt B5GMG2
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