› 4bg4

X-ray diffraction
1.6Å resolution

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

Released:
DOI: 10.2210/pdb4bg4/pdb
PDB entry 4bg4 coloured by chain, front view.
PDB entry 4bg4 coloured by chain, side view.
PDB entry 4bg4 coloured by chain, top view.
Source organism: Penaeus vannamei
Primary publication:
Crystal structure of shrimp arginine kinase in binary complex with arginine-a molecular view of the phosphagen precursor binding to the enzyme.
López-Zavala AA, García-Orozco KD, Carrasco-Miranda JS, Sugich-Miranda R, Velázquez-Contreras EF, Criscitiello MF, Brieba LG, Rudiño-Piñera E, Sotelo-Mundo RR
J Bioenerg Biomembr 45 511-8 (2013)
PMID: 23873077

Function and Biology Details

Reaction catalysed: 
ATP + L-arginine = ADP + N(omega)-phospho-L-arginine
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-169430 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Arginine kinase Lit v 2.0101 Chain: A
Molecule details ›
Chain: A
Length: 356 amino acids
Theoretical weight: 40.24 KDa
Source organism: Penaeus vannamei
UniProt:
  • Canonical: Q004B5 (Residues: 1-356; Coverage: 100%)
Sequence domains:
Structure domains:
Arginine kinase Lit v 2.0101 Chain: B
Molecule details ›
Chain: B
Length: 356 amino acids
Theoretical weight: 40.24 KDa
Source organism: Penaeus vannamei
UniProt:
  • Canonical: Q004B5 (Residues: 1-356; Coverage: 100%)
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ADP 2 x ADP
Ligand ARG 2 x ARG
Ligand NO3 2 x NO3
Ligand MG 2 x MG
Ligand BME 2 x BME
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X6A
Spacegroup: P21
Unit cell:
a: 63.32Å b: 67.15Å c: 78.77Å
α: 90° β: 92.12° γ: 90°
R-values:
R R work R free
0.193 0.191 0.225

Quick links

Citations

1 review citation

Natural Products Containing 'Rare' Organophosphorus Functional Groups.
Petkowski et al. (2019)
11 other articles

3 mentions without citation

Conservation Analysis of B-Cell Allergen Epitopes to Predict Clinical Cross-Reactivity Between Shellfish and Inhalant Invertebrate Allergens.
Nugraha et al. (2019)
2 more