MolNFT v1 · #122334 · protein
Tobacco 5-epi-aristolochene synthase with bis-tris buffer molecule and diphosphate (ppi)
5ILY: “Tobacco 5-epi-aristolochene synthase with bis-tris buffer molecule and diphosphate (ppi)”. X-ray diffraction, 2 ligands (DPO, MG), 8 pockets (best druggability 0.84). MolNFT v1 #122334 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ILY
- 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
- DPO, MG
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5-epi-aristolochene synthase (EC 4.2.3.61) | protein | 536 | 70% helix, 0% strand | Q40577 |
Ligands and binding sites
- DPO · Diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.84 | 0.93 | 50 | MG, BTB, DPO |
| 2 | 506 | 0.80 | 0.87 | 49 | empty |
| 3 | 225 | 0.58 | 0.79 | 28 | empty |
| 4 | 275 | 0.56 | 0.77 | 29 | empty |
| 5 | 75 | 0.48 | 0.83 | 16 | empty |
Compared structures
- 5ILY · Tobacco 5-epi-aristolochene synthase with BIS-TRIS buffer molecule and diphosphate (PPi) · 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 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 Q40577
- Elsewhere: RCSB PDB 5ILY · PDBe 5ILY · UniProt Q40577
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