MolNFT v1 · #189336 · protein
Crystal structure of hydroxynitrile lyase from linum usitatissium complexed with (R)-2-hydroxy-2-methylbutanenitrile
7VB6 · Aliphatic (R)-hydroxynitrile lyase: “Crystal structure of hydroxynitrile lyase from linum usitatissium complexed with…”. X-ray diffraction, 4 ligands (NAD, 5Z9, ZN), 17 pockets (best druggability 0.77). MolNFT v1 #189336 on…
- PDB
- 7VB6
- Type
- protein
- Length
- 1,638 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aliphatic (R)-hydroxynitrile lyase
- EC
- 4.1.2.46
- UniProt
- P93243
- Ligands
- NAD, 5Z9, ZN, MG
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Aliphatic (R)-hydroxynitrile lyase (EC 4.1.2.46) | protein | 408 | 30% helix, 24% strand | P93243 |
| B | Aliphatic (R)-hydroxynitrile lyase (EC 4.1.2.46) | protein | 414 | 29% helix, 23% strand | P93243 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 5Z9 · (2R)-2-methyl-2-oxidanyl-butanenitrile · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, D
- GOL · Glycerol · additive · 4 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.77 | 0.84 | 71 | NAD, MG, 5Z9 |
| 2 | 429 | 0.76 | 0.85 | 55 | NAD, 5Z9 |
| 3 | 504 | 0.76 | 0.84 | 68 | NAD, MG, 5Z9 |
| 4 | 466 | 0.75 | 0.84 | 55 | NAD, 5Z9 |
| 5 | 620 | 0.67 | 0.76 | 56 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1902 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1861 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 246 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 121 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 32 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 7VB6 · Crystal structure of hydroxynitrile lyase from Linum usitatissium complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- P93243 · AlphaFold monomer V2.0 prediction for aliphatic (R)-hydroxynitrile lyase (P93243) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P93243
- Elsewhere: RCSB PDB 7VB6 · PDBe 7VB6 · UniProt P93243
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