› 3ko9

X-ray diffraction
2.75Å resolution

DTD from Plasmodium falciparum in complex with D-Arginine

Released:
DOI: 10.2210/pdb3ko9/pdb
PDB entry 3ko9 coloured by chain, front view.
PDB entry 3ko9 coloured by chain, side view.
PDB entry 3ko9 coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Ligand-bound structures provide atomic snapshots for the catalytic mechanism of D-amino acid deacylase.
Bhatt TK, Yogavel M, Wydau S, Berwal R, Sharma A
OpenAccess logo J Biol Chem 285 5917-30 (2010)
PMID: 20007323

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
Molecule details ›
Chains: A, B, C, D, E, F
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 DAR 1 x DAR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P1
Unit cell:
a: 52.252Å b: 54.863Å c: 92.419Å
α: 106.94° β: 101.63° γ: 94.49°
R-values:
R R work R free
0.205 0.201 0.275
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Recent advances in the biology and drug targeting of malaria parasite aminoacyl-tRNA synthetases.
Khan S. (2016)
3 more

3 mentions without citation

Carboxylic ester hydrolases: Classification and database derived from their primary, secondary, and tertiary structures.
Chen et al. (2016)
2 more