MolNFT v1 · #168567 · protein
Crystal structure of pentalenene synthase mutant F76Y complexed with 12,13-difluorofarnesyl diphosphate
6WKF: “Crystal structure of pentalenene synthase mutant F76Y complexed with 12,13-difluorofarnesyl diphosphate”. X-ray diffraction, 1 ligand (FDF), 4 pockets (best druggability 0.80). MolNFT v1 #168567 on GenesisL1: 3D structure, binding…
- PDB
- 6WKF
- Type
- protein
- Length
- 572 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pentalenene synthase
- EC
- 4.2.3.7
- UniProt
- Q55012
- Ligands
- FDF
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pentalenene synthase (EC 4.2.3.7) | protein | 269 | 72% helix, 0% strand | Q55012 |
| B | Pentalenene synthase (EC 4.2.3.7) | protein | 303 | 74% helix, 0% strand | Q55012 |
Ligands and binding sites
- FDF · (2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.80 | 0.82 | 79 | empty |
| 2 | 583 | 0.76 | 0.82 | 58 | empty |
| 3 | 295 | 0.65 | 0.81 | 33 | FDF |
| 4 | 77 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 908 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6WKF · Crystal structure of pentalenene synthase mutant F76Y complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q55012 · AlphaFold monomer V2.0 prediction for pentalenene synthase (Q55012) · a predicted model of the same protein · chain B 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 Q55012
- Elsewhere: RCSB PDB 6WKF · PDBe 6WKF · UniProt Q55012
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