Research workbench
Crystal structure of the hydroxynitrile lyase from almond
Analyse Crystal structure of the hydroxynitrile lyase from almond in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JU2
- Type
- protein
- Length
- 1,042 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxynitrile lyase
- EC
- 4.1.2.10
- Ligands
- FAD, NAG, BMA, FUC, MAN, NDG
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hydroxynitrile lyase (EC 4.1.2.10) | protein | 521 | 28% helix, 26% strand | — |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 5 copies
- FUC · alpha-L-fucopyranose · sugar · 4 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A, B
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains A
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.85 | 0.90 | 90 | FAD |
| 2 | 624 | 0.85 | 0.90 | 92 | FAD |
| 3 | 455 | 0.66 | 0.78 | 39 | empty |
| 4 | 454 | 0.66 | 0.78 | 46 | empty |
| 5 | 147 | 0.49 | 0.78 | 32 | IPA |
Interfaces
1 interface between chains.
- A–B · 545 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
- 1JU2 · Crystal structure of the hydroxynitrile lyase from almond · 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
- Elsewhere: RCSB PDB 1JU2 · PDBe 1JU2
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