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Co-crystal structure of wt 5-epi-aristolochene synthase from nicotiana tobaccum with geraniline
Analyse Co-crystal structure of wt 5-epi-aristolochene synthase from nicotiana tobaccum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DI5
- Type
- protein
- Length
- 535 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
- 1GA, DPO, MG
- Pockets
- 7 · best druggability 0.81
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 | 535 | 70% helix, 0% strand | Q40577 |
Ligands and binding sites
- 1GA · Geraniline · ligand · chains A
- DPO · Diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.81 | 0.87 | 52 | empty |
| 2 | 523 | 0.80 | 0.87 | 58 | 1GA, MG, DPO |
| 3 | 234 | 0.56 | 0.78 | 27 | empty |
| 4 | 266 | 0.54 | 0.76 | 25 | empty |
| 5 | 78 | 0.49 | 0.83 | 15 | empty |
Compared structures
- 4DI5 · Co-crystal structure of WT 5-epi-Aristolochene synthase from Nicotiana tobaccum with… · 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 4DI5 · PDBe 4DI5 · UniProt Q40577
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