Crystal structure of litopenaeus vannamei arginine kinase in a ternary analog complex with arginine, ADP-mg and NO3

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Ligands and binding sites

• ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
• ARG · Arginine · ligand · 2 copies · chains A, B
• MG · Magnesium ion · metal · 2 copies · chains A, B
• NO3 · Nitrate ion · ion · 2 copies · chains A, B
• BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 923 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 2 modified (additive adduct, oxidation).

Compared structures

• 4BG4 · Crystal structure of Litopenaeus vannamei arginine kinase in a ternary analog complex… · the same entry in another collection · chain B against B, TM-score 1.00
• Q004B5 · AlphaFold monomer V2.0 prediction for arginine kinase lit V 2.0101 (Q004B5) · a predicted model of the same protein · chain B against A, TM-score 0.91

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 Q004B5
• Elsewhere: RCSB PDB 4BG4 · PDBe 4BG4 · UniProt Q004B5