MolNFT v1 · #122361 · protein
Crystal structure of N299A aspergillus terreus aristolochene synthase complexed with (1S,8S,9AR)-1,9A-dimethyl-8-(prop-1-en-2-yl) decahydroquinolizin-5-ium
5IMP: “Crystal structure of N299A aspergillus terreus aristolochene synthase complexed with…”. X-ray diffraction, 3 ligands (POP, JF1, MG), 14 pockets (best druggability 0.84). MolNFT v1 #122361 on GenesisL1: 3D structure, binding sites…
- PDB
- 5IMP
- Type
- protein
- Length
- 1,216 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
- POP, JF1, MG
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Aristolochene synthase (EC 4.2.3.9) | protein | 304 | 75% helix, 0% strand | Q9UR08 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
- JF1 · (1S,5S,8S,9aR)-1,9a-dimethyl-8-(prop-1-en-2-yl)octahydro-2H-quinolizinium · 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, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.84 | 0.95 | 44 | POP, MG, JF1 |
| 2 | 264 | 0.84 | 0.95 | 44 | POP, MG, JF1 |
| 3 | 259 | 0.84 | 0.95 | 40 | POP, MG, JF1 |
| 4 | 262 | 0.83 | 0.95 | 43 | POP, MG, JF1 |
| 5 | 619 | 0.70 | 0.78 | 55 | empty |
Interfaces
4 interfaces between chains.
- A–B · 282 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 161 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 76 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 20 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IMP · Crystal structure of N299A Aspergillus terreus aristolochene synthase 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 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 Q9UR08
- Elsewhere: RCSB PDB 5IMP · PDBe 5IMP · UniProt Q9UR08
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