5ZDK

Crystal Structure Analysis of TtQRS in complex with ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and functional analysis of Glutaminyl-tRNA synthetase (TtGlnRS) from Thermus thermophilus HB8 and its complexes

Nachiappan, M.Jain, V.Sharma, A.Yogavel, M.Jeyakanthan, J.

(2018) Int J Biol Macromol 120: 1379-1386

  • DOI: https://doi.org/10.1016/j.ijbiomac.2018.09.115
  • Primary Citation of Related Structures:  
    5ZDK, 5ZDL, 5ZDO

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases (AaRSs) are vital enzymes for translation of proteins in cells. AaRSs catalyse the esterification of a specific amino acid to corresponding tRNAs to form an aminoacyl-tRNA that is used in ribosome-based protein synthesis. We focused on Glutaminyl tRNA synthetase (GlnRS) enzyme from the extreme thermophile Thermus thermophilus for structural studies. Our thermal shift assays show binding of enzyme substrates L-Gln and ATP as well as of various metals including cesium. We resolved crystal structures of apo-GlnRS as well as those in complex with AMP and ATP at 2.8 Å, 2.4 Å and 2.6 Å respectively. The bound cesium was found at the site of magnesium that typically binds to GlnRS. High structural conservation was evident in the Thermus thermophilus GlnRS when compared to those from Escherichia coli GlnRS.


  • Organizational Affiliation

    Structural Biology and Bio-Computing Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi 630 003, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamine--tRNA ligase548Thermus thermophilus HB8Mutation(s): 0 
Gene Names: TTHA0549
EC: 6.1.1.18
UniProt
Find proteins for Q5SKU4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SKU4 
Go to UniProtKB:  Q5SKU4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SKU4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CS
Query on CS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.66α = 90
b = 39.413β = 116.48
c = 116.051γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description