MolNFT v1 · #64789 · protein
Hydroxynitrile lyase from almond, monoclinic crystal form
3GDP · R-oxynitrile lyase isoenzyme 1: “Hydroxynitrile lyase from almond, monoclinic crystal form”. X-ray diffraction, 7 ligands (FAD, NAG, MAN), 5 pockets (best druggability 0.85). MolNFT v1 #64789 on GenesisL1: 3D structure, binding…
- PDB
- 3GDP
- 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
- FAD, NAG, MAN, FUC, BMA, FUL, NDG
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 28% 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 | 28% helix, 27% strand | Q945K2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
- FUL · beta-L-fucopyranose · sugar
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
- 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
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.85 | 0.90 | 91 | FAD |
| 2 | 1069 | 0.84 | 0.85 | 135 | FAD |
| 3 | 165 | 0.51 | 0.78 | 32 | IPA |
| 4 | 168 | 0.50 | 0.77 | 36 | IPA, NAG |
| 5 | 50 | 0.25 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 3GDP · PDBe 3GDP · UniProt Q945K2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.