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Crystal structure of onion lachrymatory factor synthase (lfs) containing glycerol
Analyse Crystal structure of onion lachrymatory factor synthase (lfs) containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GTF
- 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
- SO4
- Pockets
- 6 · best druggability 0.65
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
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, D, C
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains 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 | 453 | 0.65 | 0.78 | 47 | empty |
| 2 | 405 | 0.62 | 0.77 | 50 | empty |
| 3 | 183 | 0.56 | 0.81 | 32 | empty |
| 4 | 94 | 0.41 | 0.78 | 21 | GOL |
| 5 | 63 | 0.34 | 0.77 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 847 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 434 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 35 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5GTF · Crystal structure of onion lachrymatory factor synthase (LFS) containing glycerol · 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 5GTF · PDBe 5GTF · UniProt P59082
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