Research workbench
Crystal structure of the L74F/M78V/I80V/L114F mutant of leh complexed with cyclopentene oxide
Analyse Crystal structure of the L74F/M78V/I80V/L114F mutant of leh complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YQT
- Type
- protein
- Length
- 1,139 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
- 3ZS
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 144 | 29% helix, 38% strand | Q9ZAG3 |
| D, B | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 145 | 30% helix, 37% strand | Q9ZAG3 |
| E | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 140 | 30% helix, 39% strand | Q9ZAG3 |
| F | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 141 | 33% helix, 38% strand | Q9ZAG3 |
| G | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 138 | 30% helix, 38% strand | Q9ZAG3 |
| H | Limonene-1,2-epoxide hydrolase (EC 3.3.2.8) | protein | 142 | 31% helix, 39% strand | Q9ZAG3 |
Ligands and binding sites
- 3ZS · (1R,5S)-6-oxabicyclo[3.1.0]hexane · ligand · 5 copies · chains C, D, A, B, H
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 | 599 | 0.79 | 0.85 | 72 | empty |
| 2 | 88 | 0.79 | 0.99 | 21 | 3ZS |
| 3 | 90 | 0.78 | 0.98 | 20 | 3ZS |
| 4 | 84 | 0.78 | 0.99 | 20 | 3ZS |
| 5 | 82 | 0.78 | 0.98 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1589 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1580 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1466 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1460 Ų buried · 16 hydrogen bonds · protein-protein
- D–A · 346 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5YQT · Crystal Structure of the L74F/M78V/I80V/L114F mutant of LEH complexed with cyclopentene… · the same entry in another collection · chain F against F, 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 5YQT · PDBe 5YQT · UniProt Q9ZAG3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.