Research workbench
Crystal structure of epoxide hydrolase VREH1 from vigna radiata
Analyse Crystal structure of epoxide hydrolase VREH1 from vigna radiata in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XMD
- Type
- protein
- Length
- 1,255 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epoxide hydrolase a
- UniProt
- E5L4L1
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epoxide hydrolase a | protein | 320 | 44% helix, 16% strand | E5L4L1 |
| B | Epoxide hydrolase a | protein | 322 | 44% helix, 16% strand | E5L4L1 |
| C | Epoxide hydrolase a | protein | 305 | 45% helix, 16% strand | E5L4L1 |
| D | Epoxide hydrolase a | protein | 308 | 45% helix, 17% strand | E5L4L1 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1191 | 0.83 | 0.84 | 90 | empty |
| 2 | 870 | 0.81 | 0.83 | 71 | empty |
| 3 | 881 | 0.80 | 0.82 | 68 | empty |
| 4 | 770 | 0.80 | 0.83 | 60 | empty |
| 5 | 254 | 0.48 | 0.74 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–C · 412 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 259 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 170 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XMD · Crystal structure of epoxide hydrolase VrEH1 from Vigna radiata · 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 E5L4L1
- Elsewhere: RCSB PDB 5XMD · PDBe 5XMD · UniProt E5L4L1
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