› 2ynd

X-ray diffraction
1.89Å resolution

Plasmodium vivax N-myristoyltransferase in complex with a pyrazole sulphonamide inhibitor.

Released:
DOI: 10.2210/pdb2ynd/pdb
PDB entry 2ynd coloured by chain, front view.
PDB entry 2ynd coloured by chain, side view.
PDB entry 2ynd coloured by chain, top view.
Source organism: Plasmodium vivax
Primary publication:
Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach.
Wright MH, Clough B, Rackham MD, Rangachari K, Brannigan JA, Grainger M, Moss DK, Bottrill AR, Heal WP, Broncel M, Serwa RA, Brady D, Mann DJ, Leatherbarrow RJ, Tewari R, Wilkinson AJ, Holder AA, Tate EW
Nat Chem 6 112-21 (2014)
PMID: 24451586

Function and Biology Details

Reaction catalysed: 
Tetradecanoyl-CoA + an N-terminal-glycyl-[protein] = CoA + an N-terminal-N-tetradecanoylglycyl-[protein]
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-107657 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycylpeptide N-tetradecanoyltransferase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 385 amino acids
Theoretical weight: 45.06 KDa
Source organism: Plasmodium vivax
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A5K1A2 (Residues: 26-410; Coverage: 94%)
Gene name: PVX_085815
Sequence domains:
Structure domains: Aminopeptidase

Ligands and Environments


Cofactor: Ligand NHW 3 x NHW
5 bound ligands:
Ligand DMS 3 x DMS
Ligand 646 3 x 646
Ligand SO4 1 x SO4
Ligand MG 3 x MG
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 57.45Å b: 119.05Å c: 176.73Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

30 review citations

Inverse electron demand Diels-Alder reactions in chemical biology.
Oliveira et al. (2017)
29 more

7 mentions without citation

Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT).
Salah Ud-Din et al. (2016)
6 more