MolNFT v1 · #121346 · protein
Linalool DEHYDRATASE/ISOMERASE: ldi with monoterpene substrate
5HSS: “Linalool DEHYDRATASE/ISOMERASE: ldi with monoterpene substrate”. X-ray diffraction, 2 ligands (64Z, 650), 10 pockets (best druggability 0.68). MolNFT v1 #121346 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HSS
- Type
- protein
- Length
- 1,828 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linalool DEHYDRATASE/ISOMERASE
- EC
- 4.2.1.127, 5.4.4.4
- UniProt
- E1XUJ2
- Ligands
- 64Z, 650
- Pockets
- 10 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4) | protein | 366 | 58% helix, 8% strand | E1XUJ2 |
| C, D | Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4) | protein | 365 | 58% helix, 8% strand | E1XUJ2 |
Ligands and binding sites
- 64Z · Geraniol · ligand · 3 copies · chains A, B, D, C, E
- 650 · Beta-Myrcene · ligand · 2 copies · chains B, E, C, D
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · 5 copies · chains A, B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.68 | 0.88 | 24 | PG0, 650 |
| 2 | 146 | 0.67 | 0.87 | 25 | PG0, 64Z |
| 3 | 156 | 0.67 | 0.86 | 25 | PG0, 64Z |
| 4 | 146 | 0.66 | 0.87 | 25 | PG0, 64Z |
| 5 | 133 | 0.66 | 0.87 | 24 | 650, PG0 |
Interfaces
5 interfaces between chains.
- A–B · 1194 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1192 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1187 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1183 Ų buried · 13 hydrogen bonds · protein-protein
- C–E · 1171 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5HSS · Linalool dehydratase/isomerase: Ldi with monoterpene substrate · the same entry in another collection · chain B against B, TM-score 1.00
- E1XUJ2 · AlphaFold monomer V2.0 prediction for linalool DEHYDRATASE/ISOMERASE (E1XUJ2) · a predicted model of the same protein · 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 E1XUJ2
- Elsewhere: RCSB PDB 5HSS · PDBe 5HSS · UniProt E1XUJ2
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