MolNFT v1 · #165046 · protein
Linalool dehydratase isomerase M125A mutant
6THM · Linalool dehydratase-isomerase protein ldi: “Linalool dehydratase isomerase M125A mutant”. X-ray diffraction, 11 pockets (best druggability 0.71). MolNFT v1 #165046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6THM
- Type
- protein
- Length
- 1,825 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linalool dehydratase-isomerase protein ldi
- UniProt
- W8X534
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Linalool dehydratase-isomerase protein ldi | protein | 364 | 56% helix, 7% strand | W8X534 |
| C | Linalool dehydratase-isomerase protein ldi | protein | 365 | 56% helix, 7% strand | W8X534 |
| D | Linalool dehydratase-isomerase protein ldi | protein | 368 | 56% helix, 7% strand | W8X534 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, C, B, D, E
- MLI · Malonate ion · additive · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.71 | 0.89 | 32 | empty |
| 2 | 170 | 0.70 | 0.88 | 31 | EDO |
| 3 | 171 | 0.70 | 0.88 | 33 | EDO |
| 4 | 162 | 0.69 | 0.88 | 33 | empty |
| 5 | 162 | 0.69 | 0.88 | 33 | EDO |
Interfaces
5 interfaces between chains.
- B–E · 1150 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1150 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1142 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1125 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1119 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6THM · Linalool Dehydratase Isomerase M125A mutant · 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 W8X534
- Elsewhere: RCSB PDB 6THM · PDBe 6THM · UniProt W8X534
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