Research workbench
On the mechanism of cyanogenesis catalyzed by hydroxynitrile lyase from manihot esculenta. crystal structure of active site mutant SER80ALA in complex with acetone cyanohydrin
Analyse On the mechanism of cyanogenesis catalyzed by hydroxynitrile lyase from manihot… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E89
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxynitrile lyase
- EC
- 4.2.1.37
- UniProt
- P52705
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxynitrile lyase (EC 4.2.1.37) | protein | 262 | 40% helix, 19% strand | P52705 |
| B | Hydroxynitrile lyase (EC 4.2.1.37) | protein | 258 | 42% helix, 17% strand | P52705 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.44 | 0.75 | 32 | empty |
| 2 | 164 | 0.43 | 0.74 | 24 | empty |
| 3 | 55 | 0.25 | 0.72 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 907 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1E89 · On the mechanism of cyanogenesis catalyzed by hydroxynitrile lyase from manihot… · the same entry in another collection · chain A against A, TM-score 1.00
- P52705 · AlphaFold monomer V2.0 prediction for (S)-hydroxynitrile lyase (P52705) · a predicted model of the same protein · chain B 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 P52705
- Elsewhere: RCSB PDB 1E89 · PDBe 1E89 · UniProt P52705
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