MolNFT v1 · #122641 · protein
Crystal structure of aspergillus terreus aristolochene synthase N299A complexed with farnesyl thiolodiphosphate
5IVG: “Crystal structure of aspergillus terreus aristolochene synthase N299A complexed with farnesyl…”. X-ray diffraction, 2 ligands (FPS, MG), 13 pockets (best druggability 0.85). MolNFT v1 #122641 on GenesisL1: 3D structure, binding…
- PDB
- 5IVG
- Type
- protein
- Length
- 1,218 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
- FPS, MG
- Pockets
- 13 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Aristolochene synthase (EC 4.2.3.9) | protein | 305 | 75% helix, 0% strand | Q9UR08 |
| B, C | Aristolochene synthase (EC 4.2.3.9) | protein | 304 | 75% helix, 0% strand | Q9UR08 |
Ligands and binding sites
- FPS · S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 12 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.85 | 0.96 | 42 | MG, FPS |
| 2 | 272 | 0.85 | 0.96 | 43 | MG, FPS |
| 3 | 267 | 0.85 | 0.96 | 43 | MG, FPS |
| 4 | 272 | 0.84 | 0.95 | 44 | MG, FPS |
| 5 | 286 | 0.65 | 0.81 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 870 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 860 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 103 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5IVG · Crystal structure of Aspergillus terreus aristolochene synthase N299A complexed with… · 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 A 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 Q9UR08
- Elsewhere: RCSB PDB 5IVG · PDBe 5IVG · UniProt Q9UR08
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