Research workbench
Structure of the hydroxynitrile lyase from arabidopsis thaliana
Analyse Structure of the hydroxynitrile lyase from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DQZ
- Type
- protein
- Length
- 1,022 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-hydroxynitrile lyase-like protein
- UniProt
- Q9LFT6
- Ligands
- CL
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha-hydroxynitrile lyase-like protein | protein | 256 | 39% helix, 19% strand | Q9LFT6 |
| B, D | Alpha-hydroxynitrile lyase-like protein | protein | 255 | 38% helix, 20% strand | Q9LFT6 |
Ligands and binding sites
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.69 | 0.87 | 32 | empty |
| 2 | 180 | 0.68 | 0.87 | 32 | empty |
| 3 | 182 | 0.68 | 0.86 | 32 | empty |
| 4 | 173 | 0.67 | 0.86 | 31 | empty |
| 5 | 127 | 0.35 | 0.72 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 898 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 891 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 128 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3DQZ · Structure of the hydroxynitrile lyase from Arabidopsis thaliana · the same entry in another collection · chain A against A, TM-score 1.00
- Q9LFT6 · AlphaFold monomer V2.0 prediction for alpha-hydroxynitrile lyase (Q9LFT6) · a predicted model of the same protein · 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 Q9LFT6
- Elsewhere: RCSB PDB 3DQZ · PDBe 3DQZ · UniProt Q9LFT6
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