Research workbench
Crystal structure of onion lachrymatory factor synthase (lfs), solute- free form
Analyse Crystal structure of onion lachrymatory factor synthase (lfs), solute- free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GTE
- Type
- protein
- Length
- 604 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lachrymatory-factor synthase
- EC
- 5.3.-.-
- UniProt
- P59082
- Ligands
- GLC, SO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lachrymatory-factor synthase (EC 5.3.-.-) | protein | 149 | 27% helix, 46% strand | P59082 |
| C, D | Lachrymatory-factor synthase (EC 5.3.-.-) | protein | 153 | 27% helix, 44% strand | P59082 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.62 | 0.78 | 41 | empty |
| 2 | 410 | 0.61 | 0.76 | 42 | empty |
| 3 | 172 | 0.55 | 0.80 | 32 | empty |
| 4 | 123 | 0.43 | 0.77 | 23 | empty |
| 5 | 90 | 0.32 | 0.73 | 13 | GLC |
Interfaces
4 interfaces between chains.
- A–B · 830 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 431 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 416 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GTE · Crystal structure of onion lachrymatory factor synthase (LFS), solute-free form · the same entry in another collection · chain A against A, TM-score 1.00
- P59082 · AlphaFold monomer V2.0 prediction for lachrymatory-factor synthase (P59082) · 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 P59082
- Elsewhere: RCSB PDB 5GTE · PDBe 5GTE · UniProt P59082
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