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Crystal structure of of limonene synthase with 2-fluorolinalyl DIPHOSPHATE(FLPP)
Analyse Crystal structure of of limonene synthase with 2-fluorolinalyl DIPHOSPHATE(FLPP) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ONH
- Type
- protein
- Length
- 1,086 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4S-limonene synthase
- UniProt
- Q40322
- Ligands
- F3P, MN
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4S-limonene synthase | protein | 543 | 70% helix, 0% strand | Q40322 |
Ligands and binding sites
- F3P · (1S)-1-[(1S)-1-fluoroethyl]-1,5-dimethylhexyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 6 copies · chains A, B
- 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
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.82 | 0.96 | 32 | MN, F3P |
| 2 | 252 | 0.80 | 0.92 | 33 | MN, F3P |
| 3 | 594 | 0.75 | 0.81 | 37 | empty |
| 4 | 452 | 0.72 | 0.82 | 38 | empty |
| 5 | 313 | 0.72 | 0.85 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 1158 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2ONH · Crystal Structure of of limonene synthase with 2-fluorolinalyl diphosphate(FLPP) · the same entry in another collection · 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 Q40322
- Elsewhere: RCSB PDB 2ONH · PDBe 2ONH · UniProt Q40322
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