Research workbench
Tobacco 5-epi-aristolochene synthase M4 mutant with (-)- premnaspirodiene
Analyse Tobacco 5-epi-aristolochene synthase M4 mutant with (-)- premnaspirodiene in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IKH
- Type
- protein
- Length
- 536 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5-epi-aristolochene synthase
- EC
- 4.2.3.61
- UniProt
- Q40577
- Ligands
- 6BW, MG
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-epi-aristolochene synthase (EC 4.2.3.61) | protein | 536 | 71% helix, 0% strand | Q40577 |
Ligands and binding sites
- 6BW · (2R,5S,10R)-6,10-dimethyl-2-(prop-1-en-2-yl)spiro[4.5]dec-6-ene · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.83 | 0.86 | 63 | 6BW, MG |
| 2 | 485 | 0.80 | 0.87 | 44 | empty |
| 3 | 276 | 0.55 | 0.77 | 32 | empty |
| 4 | 203 | 0.55 | 0.78 | 25 | empty |
| 5 | 102 | 0.50 | 0.82 | 16 | empty |
Compared structures
- 5IKH · Tobacco 5-epi-aristolochene synthase M4 mutant with (-)-premnaspirodiene · the same entry in another collection · chain A against A, TM-score 1.00
- Q40577 · AlphaFold monomer V2.0 prediction for 5-epi-aristolochene synthase (Q40577) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q40577
- Elsewhere: RCSB PDB 5IKH · PDBe 5IKH · UniProt Q40577
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