MolNFT v1 · #60188 · protein
Crystal structure of aristolochene synthase in complex with 12,13- difluorofarnesyl diphosphate
3CKE: “Crystal structure of aristolochene synthase in complex with 12,13- difluorofarnesyl diphosphate”. X-ray diffraction, 4 ligands (FDF, POP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #60188 on GenesisL1: 3D structure, binding…
- PDB
- 3CKE
- Type
- protein
- Length
- 1,171 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aristolochene synthase
- EC
- 4.2.3.9
- UniProt
- Q9UR08
- Ligands
- FDF, POP, MG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aristolochene synthase (EC 4.2.3.9) | protein | 295 | 71% helix, 0% strand | Q9UR08 |
| B | Aristolochene synthase (EC 4.2.3.9) | protein | 297 | 71% helix, 0% strand | Q9UR08 |
| D | Aristolochene synthase (EC 4.2.3.9) | protein | 284 | 68% helix, 0% strand | Q9UR08 |
Ligands and binding sites
- FDF · (2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate · ligand · 3 copies · chains A, B, C
- POP · Pyrophosphate 2- · ligand · chains D
- MG · Magnesium ion · metal · 2 copies · chains D
- CL · Chloride ion · ion · chains A, D
- BME · Beta-mercaptoethanol · additive · 2 copies · chains B, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.83 | 0.84 | 119 | FDF |
| 2 | 242 | 0.82 | 0.95 | 33 | empty |
| 3 | 348 | 0.77 | 0.87 | 40 | POP, MG |
| 4 | 438 | 0.75 | 0.84 | 32 | FDF |
| 5 | 358 | 0.75 | 0.86 | 29 | FDF |
Interfaces
6 interfaces between chains.
- B–C · 874 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 861 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 737 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 632 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 415 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3CKE · Crystal structure of aristolochene synthase in complex with 12,13-difluorofarnesyl… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9UR08 · AlphaFold monomer V2.0 prediction for aristolochene synthase (Q9UR08) · a predicted model of the same protein · chain D against A, TM-score 0.95
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 Q9UR08
- Elsewhere: RCSB PDB 3CKE · PDBe 3CKE · UniProt Q9UR08
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.