MolNFT v1 · #105600 · protein
Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from rhodococcus erythropolis, containing two stabilizing disulfide bonds
4R9L · Limonene-1,2-epoxide hydrolase: “Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from rhodococcus erythropolis…”. X-ray diffraction, 1 ligand (HYH), 8 pockets (best druggability 0.78). MolNFT v1 #105600…
- PDB
- 4R9L
- Type
- protein
- Length
- 460 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Limonene-1,2-epoxide hydrolase
- EC
- 3.3.2.8
- UniProt
- Q9ZAG3
- Ligands
- HYH
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 147 | 29% helix, 37% strand | Q9ZAG3 |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 153 | 33% helix, 35% strand | Q9ZAG3 |
| C | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 160 | 37% helix, 34% strand | Q9ZAG3 |
Ligands and binding sites
- HYH · (2R)-2-hydroxyhexanamide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 89 | 0.78 | 0.98 | 22 | HYH |
| 2 | 86 | 0.78 | 0.98 | 21 | HYH |
| 3 | 91 | 0.76 | 0.96 | 23 | HYH |
| 4 | 253 | 0.54 | 0.77 | 35 | empty |
| 5 | 102 | 0.38 | 0.75 | 25 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1624 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 420 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4R9L · Structure of a thermostable elevenfold mutant of limonene epoxide hydrolase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9ZAG3 · AlphaFold monomer V2.0 prediction for limonene-1,2-epoxide hydrolase (Q9ZAG3) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9ZAG3
- Elsewhere: RCSB PDB 4R9L · PDBe 4R9L · UniProt Q9ZAG3
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