Research workbench
Crystal structure of F128A mutant of an epoxide hydrolase from bacillus megaterium complexed with its product (R)-3-[1]NAPHTHYLOXY- propane-1,2-diol
Analyse Crystal structure of F128A mutant of an epoxide hydrolase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IO0
- Type
- protein
- Length
- 572 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
- RN1, SO4
- Pockets
- 7 · best druggability 0.77
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 | 288 | 48% helix, 17% strand | G9BEX6 |
| B | Soluble epoxide hydrolase (EC 3.2.2.10) | protein | 284 | 49% helix, 16% strand | G9BEX6 |
Ligands and binding sites
- RN1 · (2R)-3-(naphthalen-1-yloxy)propane-1,2-diol · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.77 | 0.96 | 19 | RN1 |
| 2 | 92 | 0.76 | 0.97 | 21 | RN1 |
| 3 | 193 | 0.57 | 0.80 | 28 | empty |
| 4 | 182 | 0.55 | 0.80 | 28 | empty |
| 5 | 166 | 0.53 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4IO0 · Crystal structure of F128A mutant of an epoxide hydrolase from Bacillus megaterium… · 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 4IO0 · PDBe 4IO0 · UniProt G9BEX6
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