Research workbench
Crystal structure of S303A aspergillus terreus aristolochene synthase complexed with (1S,8S,9AR)-1,9A-dimethyl-8-(prop-1-en-2-yl) decahydroquinolizin-5-ium
Analyse Crystal structure of S303A aspergillus terreus aristolochene synthase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IMI
- Type
- protein
- Length
- 1,222 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
- 16 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Aristolochene synthase (EC 4.2.3.9) | protein | 306 | 74% helix, 0% strand | Q9UR08 |
| B | Aristolochene synthase (EC 4.2.3.9) | protein | 306 | 74% helix, 0% strand | Q9UR08 |
| C | Aristolochene synthase (EC 4.2.3.9) | protein | 304 | 74% 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 · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.84 | 0.96 | 41 | POP, MG, JF1 |
| 2 | 268 | 0.84 | 0.96 | 40 | POP, MG, JF1 |
| 3 | 237 | 0.84 | 0.96 | 42 | POP, MG, JF1 |
| 4 | 259 | 0.83 | 0.95 | 41 | POP, MG, JF1 |
| 5 | 706 | 0.70 | 0.77 | 66 | empty |
Interfaces
4 interfaces between chains.
- A–B · 277 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 187 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 63 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 30 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5IMI · Crystal structure of S303A 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 5IMI · PDBe 5IMI · UniProt Q9UR08
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.