Research workbench
Crystal complex of endo-deglycosylated hydroxynitrile lyase isozyme 5 of prunus communis with benzaldehyde
Analyse Crystal complex of endo-deglycosylated hydroxynitrile lyase isozyme 5 of prunus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LQY
- Type
- protein
- Length
- 517 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Predicted: (R)-mandelonitrile lyase
- UniProt
- A0A5E4GBK6
- Ligands
- FAD, HBX, NAG
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Predicted: (R)-mandelonitrile lyase | protein | 517 | 29% helix, 27% strand | A0A5E4GBK6 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · chains A
- HBX · benzaldehyde · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.86 | 0.93 | 66 | FAD, HBX |
| 2 | 188 | 0.58 | 0.81 | 33 | empty |
| 3 | 61 | 0.34 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 7 glycan, 1 disulfide (N-glycosylation, disulfide).
Compared structures
- 6LQY · Crystal complex of endo-deglycosylated hydroxynitrile lyase isozyme 5 of Prunus communis… · 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
- Every structure of UniProt A0A5E4GBK6
- Elsewhere: RCSB PDB 6LQY · PDBe 6LQY · UniProt A0A5E4GBK6
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