MolNFT v1 · #122272 · protein
Tobacco 5-epi-aristolochene synthase with germacrene a and ppi
5IK6: “Tobacco 5-epi-aristolochene synthase with germacrene a and ppi”. X-ray diffraction, 3 ligands (CRE, DPO, MG), 6 pockets (best druggability 0.82). MolNFT v1 #122272 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5IK6
- 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
- CRE, DPO, MG
- Pockets
- 6 · best druggability 0.82
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
- CRE · Germacrene A · ligand · chains A
- DPO · Diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 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 | 549 | 0.82 | 0.88 | 54 | empty |
| 2 | 558 | 0.81 | 0.87 | 69 | MG, CRE, DPO |
| 3 | 344 | 0.59 | 0.77 | 30 | empty |
| 4 | 232 | 0.58 | 0.79 | 25 | empty |
| 5 | 96 | 0.50 | 0.82 | 17 | empty |
Compared structures
- 5IK6 · Tobacco 5-epi-aristolochene synthase with germacrene A and 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 5IK6 · PDBe 5IK6 · UniProt Q40577
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