MolNFT v1 · #168565 · protein
Crystal structure of pentalenene synthase complexed with 12,13- difluorofarnesyl diphosphate
6WKD: “Crystal structure of pentalenene synthase complexed with 12,13- difluorofarnesyl diphosphate”. X-ray diffraction, 2 ligands (FDF, MG), 4 pockets (best druggability 0.83). MolNFT v1 #168565 on GenesisL1: 3D structure, binding sites…
- PDB
- 6WKD
- Type
- protein
- Length
- 587 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, MG
- Pockets
- 4 · best druggability 0.83
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 | 280 | 73% helix, 0% strand | Q55012 |
| B | Pentalenene synthase (EC 4.2.3.7) | protein | 307 | 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
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 1092 | 0.83 | 0.84 | 80 | empty |
| 2 | 598 | 0.76 | 0.82 | 53 | empty |
| 3 | 334 | 0.70 | 0.83 | 33 | FDF, MG |
| 4 | 57 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6WKD · Crystal structure of pentalenene synthase complexed with 12,13-difluorofarnesyl… · 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 6WKD · PDBe 6WKD · UniProt Q55012
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.