Research workbench
Crystal structure of hydroxynitrile lyase from manihot esculenta at 2.2 ångström resolution
Analyse Crystal structure of hydroxynitrile lyase from manihot esculenta at 2.2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DWP
- 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
- 2 · best druggability 0.54
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, 17% strand | P52705 |
Ligands and binding sites
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.54 | 0.74 | 52 | empty |
| 2 | 55 | 0.36 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 907 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1DWP · Crystal Structure of Hydroxynitrile Lyase from Manihot esculenta at 2.2 Angstrom… · 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 1DWP · PDBe 1DWP · UniProt P52705
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