MolNFT v1 · #101729 · protein
Crystal structure of bacillus megaterium epoxide hydrolase in complex with an inhibitor
4O08 · Soluble epoxide hydrolase: “Crystal structure of bacillus megaterium epoxide hydrolase in complex with an inhibitor”. X-ray diffraction, 2 ligands (PO6, SO4), 5 pockets (best druggability 0.71). MolNFT v1 #101729 on GenesisL1: 3D…
- 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
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