MolNFT v1 · #5435 · protein
X-ray structure of the epoxide hydrolase from agrobacterium radiobacter AD1
1EHY · Protein (soluble epoxide hydrolase): “X-ray structure of the epoxide hydrolase from agrobacterium radiobacter AD1”. X-ray diffraction, 1 ligand (K), 11 pockets (best druggability 0.78). MolNFT v1 #5435 on GenesisL1: 3D structure…
- PDB
- 1EHY
- Type
- protein
- Length
- 1,128 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (soluble epoxide hydrolase)
- EC
- 3.3.2.10
- UniProt
- O31243
- Ligands
- K
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (soluble epoxide hydrolase) (EC 3.3.2.10) | protein | 282 | 44% helix, 18% strand | O31243 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.78 | 0.79 | 66 | empty |
| 2 | 1005 | 0.77 | 0.79 | 64 | empty |
| 3 | 297 | 0.56 | 0.76 | 46 | empty |
| 4 | 236 | 0.55 | 0.78 | 39 | empty |
| 5 | 228 | 0.53 | 0.77 | 37 | empty |
Interfaces
6 interfaces between chains.
- A–C · 718 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 696 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 386 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 374 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 150 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1EHY · X-ray structure of the epoxide hydrolase from agrobacterium radiobacter ad1 · 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 O31243
- Elsewhere: RCSB PDB 1EHY · PDBe 1EHY · UniProt O31243
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