MolNFT v1 · #98015 · protein
Crystal structure of aspergillus terreus aristolochene synthase complexed with (1R,8R,9AS)-1,9A-dimethyl-8-(prop-1-en-2-yl) decahydroquinolizin-5-ium
4KWD: “Crystal structure of aspergillus terreus aristolochene synthase complexed with…”. X-ray diffraction, 3 ligands (POP, JF2, MG), 14 pockets (best druggability 0.85). MolNFT v1 #98015 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KWD
- 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, JF2, MG
- Pockets
- 14 · best druggability 0.85
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
- JF2 · (1R,5R,8R,9aS)-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 · 2 copies · chains B, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.85 | 0.96 | 41 | POP, MG, JF2 |
| 2 | 273 | 0.85 | 0.96 | 43 | POP, MG, JF2 |
| 3 | 255 | 0.84 | 0.96 | 41 | MG, POP, JF2 |
| 4 | 258 | 0.84 | 0.96 | 41 | POP, MG, JF2 |
| 5 | 229 | 0.56 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 902 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 882 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 95 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4KWD · Crystal structure of 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 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 4KWD · PDBe 4KWD · UniProt Q9UR08
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