Research workbench
Athnl enantioselectivity mutant at-A9-H7 apo, Y13C,Y121L,P126F,L128W, C131T,F179L,A209I with benzaldehyde
Analyse Athnl enantioselectivity mutant at-A9-H7 apo, Y13C,Y121L,P126F,L128W… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6COC
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-hydroxynitrile lyase
- EC
- 4.1.2.10
- UniProt
- Q9LFT6
- Ligands
- HBX, CL
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-hydroxynitrile lyase (EC 4.1.2.10) | protein | 260 | 40% helix, 18% strand | Q9LFT6 |
| B | Alpha-hydroxynitrile lyase (EC 4.1.2.10) | protein | 259 | 40% helix, 19% strand | Q9LFT6 |
Ligands and binding sites
- HBX · benzaldehyde · ligand · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.78 | 0.99 | 19 | CL |
| 2 | 77 | 0.76 | 0.98 | 17 | CL, HBX |
| 3 | 95 | 0.31 | 0.72 | 18 | empty |
| 4 | 80 | 0.29 | 0.72 | 15 | empty |
| 5 | 54 | 0.25 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 990 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6COC · AtHNL enantioselectivity mutant At-A9-H7 Apo, Y13C,Y121L,P126F,L128W,C131T,F179L,A209I… · 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 B against A, TM-score 0.99
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 6COC · PDBe 6COC · UniProt Q9LFT6
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