MolNFT v1 · #109743 · protein
Crystal structure of the L74F/M78F/L103V/L114V/I116V/F139V/L147V mutant of leh complexed with (S,S)-cyclohexanediol
4XBT · Limonene-1,2-epoxide hydrolase: “Crystal structure of the L74F/M78F/L103V/L114V/I116V/F139V/L147V mutant of leh complexed with…”. X-ray diffraction, 1 ligand (3ZQ), 11 pockets (best druggability 0.80). MolNFT v1 #109743 on…
- PDB
- 4XBT
- Type
- protein
- Length
- 587 residues
- Chains
- 4
- 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
- 3ZQ
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 149 | 28% helix, 36% strand | Q9ZAG3 |
| B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 144 | 33% helix, 38% strand | Q9ZAG3 |
| D | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 145 | 33% helix, 37% strand | Q9ZAG3 |
Ligands and binding sites
- 3ZQ · (1S,2S)-cyclohexane-1,2-diol · ligand · 2 copies · chains A, C
- FLC · Citrate anion · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1130 | 0.80 | 0.81 | 88 | 3ZQ |
| 2 | 157 | 0.69 | 0.87 | 25 | FLC |
| 3 | 166 | 0.69 | 0.87 | 30 | 3ZQ |
| 4 | 149 | 0.68 | 0.88 | 26 | FLC |
| 5 | 89 | 0.38 | 0.76 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1713 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1712 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 354 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4XBT · Crystal Structure of the L74F/M78F/L103V/L114V/I116V/F139V/L147V mutant of LEH complexed… · 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 B 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 Q9ZAG3
- Elsewhere: RCSB PDB 4XBT · PDBe 4XBT · UniProt Q9ZAG3
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