› 4nbj

X-ray diffraction
2.2Å resolution

D-aminoacyl-tRNA deacylase (DTD) from Plasmodium falciparum in complex with D-tyrosyl-3'-aminoadenosine at 2.20 Angstrom resolution

Released:
DOI: 10.2210/pdb4nbj/pdb
PDB entry 4nbj coloured by chain, front view.
PDB entry 4nbj coloured by chain, side view.
PDB entry 4nbj coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Mechanism of chiral proofreading during translation of the genetic code.
Ahmad S, Routh SB, Kamarthapu V, Chalissery J, Muthukumar S, Hussain T, Kruparani SP, Deshmukh MV, Sankaranarayanan R
Elife 2 e01519 (2013)
PMID: 24302572

Function and Biology Details

Reaction catalysed: 
A D-aminoacyl-tRNA + H(2)O = a D-amino acid + tRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184791 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-aminoacyl-tRNA deacylase Chains: A, B, C, D, E, F, G, H
Molecule details ›
Chains: A, B, C, D, E, F, G, H
Length: 164 amino acids
Theoretical weight: 19.23 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IIS0 (Residues: 1-164; Coverage: 100%)
Gene names: DTD, PF11_0095, PF3D7_1108200
Sequence domains: D-Tyr-tRNA(Tyr) deacylase
Structure domains: D-tyrosyl-tRNA(Tyr) deacylase

Ligands and Environments

1 bound ligand:
Ligand D3Y 8 x D3Y
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P21
Unit cell:
a: 90.901Å b: 79.907Å c: 95.023Å
α: 90° β: 93.51° γ: 90°
R-values:
R R work R free
0.198 0.194 0.254
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Chiral checkpoints during protein biosynthesis.
Kuncha et al. (2019)
1 more

2 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
1 more