MolNFT v1 · #16277 · protein
Limonene-1,2-epoxide hydrolase in complex with valpromide
1NU3: “Limonene-1,2-epoxide hydrolase in complex with valpromide”. X-ray diffraction, 1 ligand (VPR), 4 pockets (best druggability 0.78). MolNFT v1 #16277 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1NU3
- Type
- protein
- Length
- 292 residues
- Chains
- 2
- 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
- VPR
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 145 | 30% helix, 37% strand | Q9ZAG3 |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 147 | 33% helix, 37% strand | Q9ZAG3 |
Ligands and binding sites
- VPR · 2-propylpentanamide · ligand · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.78 | 0.98 | 21 | VPR |
| 2 | 86 | 0.77 | 0.98 | 20 | VPR |
| 3 | 89 | 0.34 | 0.74 | 18 | empty |
| 4 | 59 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1663 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
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 1NU3 · PDBe 1NU3 · UniProt Q9ZAG3
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