MolNFT v1 · #109815 · protein
Crystal structure of the L74F/M78V/I80V/L114F mutant of leh complexed with cyclohexanediol
4XDV · Limonene-1,2-epoxide hydrolase: “Crystal structure of the L74F/M78V/I80V/L114F mutant of leh complexed with cyclohexanediol”. X-ray diffraction, 1 ligand (40O), 20 pockets (best druggability 0.80). MolNFT v1 #109815 on GenesisL1: 3D…
- PDB
- 4XDV
- Type
- protein
- Length
- 1,127 residues
- Chains
- 8
- 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
- 40O
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 144 | 32% helix, 38% strand | Q9ZAG3 |
| E | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 126 | 24% helix, 35% strand | Q9ZAG3 |
| G, A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 143 | 32% helix, 38% strand | Q9ZAG3 |
| D, B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 145 | 30% helix, 37% strand | Q9ZAG3 |
| F | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 140 | 29% helix, 42% strand | Q9ZAG3 |
| H | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 141 | 31% helix, 41% strand | Q9ZAG3 |
Ligands and binding sites
- 40O · (1R,2R)-cyclohexane-1,2-diol · ligand · 4 copies · chains C, D, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.80 | 0.85 | 68 | empty |
| 2 | 98 | 0.79 | 0.98 | 20 | 40O |
| 3 | 600 | 0.79 | 0.85 | 68 | empty |
| 4 | 92 | 0.79 | 0.98 | 19 | 40O |
| 5 | 91 | 0.79 | 0.98 | 20 | 40O |
Interfaces
12 interfaces between chains.
- C–D · 1552 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1547 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1530 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1475 Ų buried · 19 hydrogen bonds · protein-protein
- H–B · 206 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4XDV · Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH complexed with cyclohexanediol · the same entry in another collection · chain B against B, 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 F against A, TM-score 0.93
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 4XDV · PDBe 4XDV · UniProt Q9ZAG3
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