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Structure of thermostable eightfold mutant of limonene epoxide hydrolase from rhodococcus erythropolis
Analyse Structure of thermostable eightfold mutant of limonene epoxide hydrolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R9K
- Type
- protein
- Length
- 459 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 0.79
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 144 | 33% helix, 38% strand | Q9ZAG3 |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 155 | 39% helix, 35% strand | Q9ZAG3 |
| C | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 160 | 36% helix, 34% strand | Q9ZAG3 |
Ligands and binding sites
- HYH · (2R)-2-hydroxyhexanamide · ligand · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 5 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 | 87 | 0.79 | 0.99 | 21 | HYH |
| 2 | 84 | 0.78 | 0.98 | 24 | HYH |
| 3 | 126 | 0.69 | 0.90 | 27 | HYH |
| 4 | 235 | 0.55 | 0.77 | 31 | empty |
| 5 | 106 | 0.37 | 0.74 | 20 | GOL |
Interfaces
2 interfaces between chains.
- A–B · 1579 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 485 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4R9K · Structure of thermostable eightfold mutant of limonene epoxide hydrolase from Rhodococcus… · 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 0.99
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 Q9ZAG3
- Elsewhere: RCSB PDB 4R9K · PDBe 4R9K · UniProt Q9ZAG3
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