MolNFT v1 · #121722 · protein
Native structure of the linalool dehydratase-isomerase from castellaniella defragrans
5I3T · Linalool DEHYDRATASE/ISOMERASE: “Native structure of the linalool dehydratase-isomerase from castellaniella defragrans”. X-ray diffraction, 2 ligands (K, CL), 12 pockets (best druggability 0.68). MolNFT v1 #121722 on GenesisL1: 3D…
- PDB
- 5I3T
- Type
- protein
- Length
- 1,812 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
- K, CL
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4) | protein | 363 | 56% helix, 8% strand | E1XUJ2 |
| B, C, D | Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4) | protein | 362 | 57% helix, 7% strand | E1XUJ2 |
| E | Linalool DEHYDRATASE/ISOMERASE (EC 4.2.1.127, 5.4.4.4) | protein | 363 | 55% helix, 8% strand | E1XUJ2 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, D, B, E, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E
- BU2 · 1,3-butanediol · additive · 3 copies · chains A, D, C, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.68 | 0.88 | 26 | K, BU2 |
| 2 | 153 | 0.67 | 0.87 | 26 | K |
| 3 | 159 | 0.66 | 0.86 | 26 | BU2, K |
| 4 | 153 | 0.66 | 0.86 | 24 | BU2, K |
| 5 | 150 | 0.62 | 0.84 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–E · 1224 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1215 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1206 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 1205 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1199 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5I3T · Native Structure of the Linalool Dehydratase-Isomerase from Castellaniella defragrans · the same entry in another collection · chain E against E, 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 5I3T · PDBe 5I3T · UniProt E1XUJ2
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