› 3adc

X-ray diffraction
2.9Å resolution

Crystal structure of O-phosphoseryl-tRNA kinase complexed with selenocysteine tRNA and AMPPNP (crystal type 2)

Released:
DOI: 10.2210/pdb3adc/pdb
PDB entry 3adc coloured by chain, front view.
PDB entry 3adc coloured by chain, side view.
PDB entry 3adc coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for the major role of O-phosphoseryl-tRNA kinase in the UGA-specific encoding of selenocysteine.
Chiba S, Itoh Y, Sekine S, Yokoyama S
Mol Cell 39 410-20 (2010)
PMID: 20705242

Function and Biology Details

Reaction catalysed: 
ATP + L-seryl-tRNA(Sec) = ADP + O-phospho-L-seryl-tRNA(Sec)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176714 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
L-seryl-tRNA(Sec) kinase Chains: A, B
Molecule details ›
Chains: A, B
Length: 259 amino acids
Theoretical weight: 31.2 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58933 (Residues: 1-248; Coverage: 100%)
Gene names: MJ1538, pstK
Sequence domains: Chromatin associated protein KTI12
Structure domains:
selenocysteine tRNA Chains: C, D
Molecule details ›
Chains: C, D
Length: 92 nucleotides
Theoretical weight: 29.71 KDa
Source organism: Methanopyrus kandleri
Expression system: Not provided
Sequence domains: Selenocysteine transfer RNA

Ligands and Environments

2 bound ligands:
Ligand ANP 2 x ANP
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 10 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21212
Unit cell:
a: 96.824Å b: 263.558Å c: 46.122Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.227 0.224 0.277
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Selenoproteins: molecular pathways and physiological roles.
Labunskyy et al. (2014)
5 more

3 mentions without citation

A nonredundant structure dataset for benchmarking protein-RNA computational docking.
Huang et al. (2013)
2 more