Research workbench
Crystal structure of the manihot esculenta hydroxynitrile lyase (mehnl) 3KP (K176P, K199P, K224P) triple mutant
Analyse Crystal structure of the manihot esculenta hydroxynitrile lyase (mehnl) 3KP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X3H
- Type
- protein
- Length
- 2,064 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (S)-hydroxynitrile lyase
- EC
- 4.1.2.47
- UniProt
- P52705
- Pockets
- 18 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | (S)-hydroxynitrile lyase (EC 4.1.2.47) | protein | 258 | 42% helix, 18% strand | P52705 |
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.74 | 0.77 | 88 | empty |
| 2 | 489 | 0.73 | 0.82 | 59 | empty |
| 3 | 397 | 0.71 | 0.83 | 44 | empty |
| 4 | 407 | 0.71 | 0.82 | 42 | empty |
| 5 | 426 | 0.70 | 0.81 | 36 | empty |
Interfaces
13 interfaces between chains.
- A–F · 887 Ų buried · 3 hydrogen bonds · protein-protein
- D–G · 885 Ų buried · 4 hydrogen bonds · protein-protein
- C–H · 882 Ų buried · 2 hydrogen bonds · protein-protein
- B–E · 881 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 471 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3X3H · Crystal Structure of the Manihot esculenta Hydroxynitrile Lyase (MeHNL) 3KP (K176P… · the same entry in another collection · chain H against H, TM-score 1.00
- P52705 · AlphaFold monomer V2.0 prediction for (S)-hydroxynitrile lyase (P52705) · 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 P52705
- Elsewhere: RCSB PDB 3X3H · PDBe 3X3H · UniProt P52705
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