Research workbench
Crystal structure of hydroxynitrile lyase from linum usitatissimum
Analyse Crystal structure of hydroxynitrile lyase from linum usitatissimum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VB3
- Type
- protein
- Length
- 1,639 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, ZN, MG
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, 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, 24% strand | P93243 |
| C | Aliphatic (R)-hydroxynitrile lyase (EC 4.1.2.46) | protein | 409 | 30% helix, 24% strand | P93243 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · 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
- GOL · Glycerol · additive · 11 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.78 | 0.85 | 71 | NAD, GOL, MG |
| 2 | 444 | 0.76 | 0.85 | 53 | NAD, GOL |
| 3 | 450 | 0.75 | 0.84 | 53 | NAD, GOL |
| 4 | 447 | 0.74 | 0.83 | 55 | NAD, GOL |
| 5 | 525 | 0.64 | 0.76 | 52 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1852 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1836 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 146 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 37 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 7VB3 · Crystal structure of hydroxynitrile lyase from Linum usitatissimum · 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 C 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 7VB3 · PDBe 7VB3 · UniProt P93243
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