Research workbench
Almond hydroxynitrile lyase in complex with benzaldehyde
Analyse Almond hydroxynitrile lyase in complex with benzaldehyde in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GDN
- Type
- protein
- Length
- 1,042 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- R-oxynitrile lyase isoenzyme 1
- EC
- 4.1.2.10
- UniProt
- Q945K2
- Ligands
- MXN, FAD, HBX, NAG, MAN, FUC, BMA
- Pockets
- 4 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | R-oxynitrile lyase isoenzyme 1 (EC 4.1.2.10) | protein | 521 | 27% helix, 27% strand | Q945K2 |
Ligands and binding sites
- MXN · (2R)-hydroxy(phenyl)ethanenitrile · ligand · 4 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- HBX · benzaldehyde · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.85 | 0.90 | 91 | FAD, HBX |
| 2 | 1119 | 0.83 | 0.84 | 130 | FAD, HBX |
| 3 | 144 | 0.50 | 0.79 | 34 | NAG, MXN |
| 4 | 154 | 0.49 | 0.78 | 31 | NAG, MXN |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 2 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q945K2
- Elsewhere: RCSB PDB 3GDN · PDBe 3GDN · UniProt Q945K2
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