MolNFT v1 · #59106 · protein
Crystal structure of aristolochene synthase complexed with farnesyl diphosphate
3BNX: “Crystal structure of aristolochene synthase complexed with farnesyl diphosphate”. X-ray diffraction, 3 ligands (FPP, POP, MG), 16 pockets (best druggability 0.83). MolNFT v1 #59106 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3BNX
- Type
- protein
- Length
- 1,179 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
- FPP, POP, MG
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aristolochene synthase (EC 4.2.3.9) | protein | 296 | 72% helix, 0% strand | Q9UR08 |
| B | Aristolochene synthase (EC 4.2.3.9) | protein | 298 | 71% helix, 0% strand | Q9UR08 |
| C | Aristolochene synthase (EC 4.2.3.9) | protein | 295 | 67% helix, 0% strand | Q9UR08 |
| D | Aristolochene synthase (EC 4.2.3.9) | protein | 290 | 73% helix, 0% strand | Q9UR08 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · 3 copies · chains A, B, C
- POP · Pyrophosphate 2- · ligand · chains D
- MG · Magnesium ion · metal · chains D
- BME · Beta-mercaptoethanol · additive · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1127 | 0.83 | 0.84 | 138 | BME |
| 2 | 202 | 0.80 | 0.95 | 33 | empty |
| 3 | 324 | 0.74 | 0.86 | 28 | FPP |
| 4 | 326 | 0.73 | 0.85 | 30 | FPP |
| 5 | 474 | 0.72 | 0.82 | 32 | FPP |
Interfaces
6 interfaces between chains.
- B–C · 857 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 857 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 728 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 564 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 430 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (additive adduct).
Compared structures
- 3BNX · Crystal structure of Aristolochene synthase complexed with farnesyl diphosphate · the same entry in another collection · chain A against A, 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 3BNX · PDBe 3BNX · UniProt Q9UR08
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