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Crystal structure of onion lachrymatory factor synthase (lfs) containing 1,2-propanediol
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
- 5GTG
- Type
- protein
- Length
- 1,192 residues
- Chains
- 8
- 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
- 10 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Lachrymatory-factor synthase (EC 5.3.-.-) | protein | 149 | 27% helix, 46% strand | P59082 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, F
- PGO · S-1,2-propanediol · additive · 4 copies · chains A, B, D, G
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1125 | 0.74 | 0.77 | 133 | empty |
| 2 | 65 | 0.68 | 0.94 | 27 | empty |
| 3 | 325 | 0.58 | 0.77 | 53 | empty |
| 4 | 317 | 0.57 | 0.77 | 34 | empty |
| 5 | 243 | 0.52 | 0.76 | 35 | empty |
Interfaces
10 interfaces between chains.
- D–E · 898 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 802 Ų buried · 11 hydrogen bonds · protein-protein
- E–H · 509 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 476 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 465 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5GTG · Crystal structure of onion lachrymatory factor synthase (LFS) containing 1,2-propanediol · the same entry in another collection · chain H against H, 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 5GTG · PDBe 5GTG · UniProt P59082
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