Research workbench
Crystal structure of bacillus megaterium epoxide hydrolase in complex with an inhibitor
Analyse Crystal structure of bacillus megaterium epoxide hydrolase in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O08
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble epoxide hydrolase
- EC
- 3.2.2.10
- UniProt
- G9BEX6
- Ligands
- PO6, SO4
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble epoxide hydrolase (EC 3.2.2.10) | protein | 287 | 48% helix, 17% strand | G9BEX6 |
| B | Soluble epoxide hydrolase (EC 3.2.2.10) | protein | 284 | 48% helix, 16% strand | G9BEX6 |
Ligands and binding sites
- PO6 · 2-phenoxyacetamide · ligand · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.71 | 0.98 | 14 | PO6 |
| 2 | 190 | 0.56 | 0.80 | 30 | PO6 |
| 3 | 158 | 0.55 | 0.81 | 31 | PO6 |
| 4 | 224 | 0.54 | 0.77 | 30 | empty |
| 5 | 55 | 0.40 | 0.81 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 657 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4O08 · Crystal structure of bacillus megaterium epoxide hydrolase in complex with an inhibitor · the same entry in another collection · chain A 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 G9BEX6
- Elsewhere: RCSB PDB 4O08 · PDBe 4O08 · UniProt G9BEX6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.