MolNFT v1 · #59107 · protein
Crystal structure of aristolochene synthase complexed with 2-fluorofarnesyl diphosphate (2F-fpp)
3BNY: “Crystal structure of aristolochene synthase complexed with 2-fluorofarnesyl diphosphate (2F-fpp)”. X-ray diffraction, 3 ligands (FPF, MG, CL), 20 pockets (best druggability 0.84). MolNFT v1 #59107 on GenesisL1: 3D structure, binding…
- PDB
- 3BNY
- Type
- protein
- Length
- 1,180 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
- FPF, MG, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aristolochene synthase (EC 4.2.3.9) | protein | 294 | 73% helix, 0% strand | Q9UR08 |
| B | Aristolochene synthase (EC 4.2.3.9) | protein | 296 | 72% helix, 0% strand | Q9UR08 |
| C | Aristolochene synthase (EC 4.2.3.9) | protein | 293 | 72% helix, 0% strand | Q9UR08 |
| D | Aristolochene synthase (EC 4.2.3.9) | protein | 297 | 72% helix, 0% strand | Q9UR08 |
Ligands and binding sites
- FPF · (2Z,6E)-2-fluoro-3,7,11-trimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · chains D
- CL · Chloride ion · ion · chains B
- BME · Beta-mercaptoethanol · additive · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.84 | 0.91 | 79 | empty |
| 2 | 902 | 0.77 | 0.80 | 71 | FPF |
| 3 | 346 | 0.74 | 0.85 | 30 | FPF |
| 4 | 384 | 0.73 | 0.84 | 27 | FPF |
| 5 | 211 | 0.72 | 0.87 | 20 | FPF |
Interfaces
6 interfaces between chains.
- B–C · 859 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 850 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 712 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 545 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (additive adduct).
Compared structures
- 3BNY · Crystal structure of aristolochene synthase complexed with 2-fluorofarnesyl diphosphate… · 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 0.94
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 3BNY · PDBe 3BNY · UniProt Q9UR08
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