MolNFT v1 · #177216 · protein
Co-crystal of kurarinone with seh
7EBA · Bifunctional epoxide hydrolase 2: “Co-crystal of kurarinone with seh”. X-ray diffraction, 1 ligand (J0U), 4 pockets (best druggability 0.84). MolNFT v1 #177216 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7EBA
- Type
- protein
- Length
- 635 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional epoxide hydrolase 2
- EC
- 3.3.2.10, 3.1.3.76
- UniProt
- P34913
- Ligands
- J0U
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional epoxide hydrolase 2 (EC 3.3.2.10, 3.1.3.76) | protein | 316 | 42% helix, 16% strand | P34913 |
| B | Bifunctional epoxide hydrolase 2 (EC 3.3.2.10, 3.1.3.76) | protein | 319 | 42% helix, 16% strand | P34913 |
Ligands and binding sites
- J0U · (2S)-2-[2,4-bis(oxidanyl)phenyl]-5-methoxy-8-[(2R)-5-methyl-2-prop-1-en-2-yl-hex-4-enyl]-7-oxidanyl-2,3-dihydrochromen-4-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.84 | 0.87 | 65 | J0U |
| 2 | 504 | 0.80 | 0.86 | 36 | J0U |
| 3 | 194 | 0.75 | 0.90 | 28 | empty |
| 4 | 58 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 766 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7EBA · Co-crystal of kurari with sEH · 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 P34913
- Elsewhere: RCSB PDB 7EBA · PDBe 7EBA · UniProt P34913
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