MolNFT v1 · #4726 · protein
Crystal structure of hydroxynitrile lyase from manihot esculenta in complex with substrates acetone and CHLOROACETONE:IMPLICATIONS for the mechanism of cyanogenesis
1DWQ: “Crystal structure of hydroxynitrile lyase from manihot esculenta in complex with substrates acetone and…”. X-ray diffraction, 1 ligand (ATO), 2 pockets (best druggability 0.42). MolNFT v1 #4726 on GenesisL1: 3D structure, binding…
- PDB
- 1DWQ
- 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
- Ligands
- ATO
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxynitrile lyase (EC 4.2.1.37) | protein | 262 | 41% helix, 18% strand | P52705 |
| B | Hydroxynitrile lyase (EC 4.2.1.37) | protein | 258 | 42% helix, 18% strand | P52705 |
Ligands and binding sites
- ATO · Chloroacetone · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.42 | 0.73 | 26 | empty |
| 2 | 100 | 0.35 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 898 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 1DWQ · Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta in Complex with… · 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 1DWQ · PDBe 1DWQ · UniProt P52705
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.