4Q2X | pdb_00004q2x

Crystal structure of Arginyl-tRNA synthetase complexed with L-canavanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.265 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

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This is version 2.0 of the entry. See complete history

Literature

The crystal structure of arginyl-tRNA synthetase from Homo sapiens

Kim, H.S.Cha, S.Y.Jo, C.H.Han, A.R.Hwang, K.Y.

(2014) FEBS Lett 588: 2328-2334

  • DOI: https://doi.org/10.1016/j.febslet.2014.05.027
  • Primary Citation Related Structures: 
    4Q2T, 4Q2X, 4Q2Y

  • PubMed Abstract: 

    Arginyl-tRNA synthetase (ArgRS) is a tRNA-binding protein that catalyzes the esterification of L-arginine to its cognate tRNA. L-Canavanine, a structural analog of L-arginine, has recently been studied as an anticancer agent. Here, we determined the crystal structures of the apo, L-arginine-complexed, and L-canavanine-complexed forms of the cytoplasmic free isoform of human ArgRS (hArgRS). Similar interactions were formed upon binding to L-canavanine or L-arginine, but the interaction between Tyr312 and the oxygen of the oxyguanidino group was a little bit different. Detailed conformational changes that occur upon substrate binding were explained. The hArgRS structure was also compared with previously reported homologue structures. The results presented here may provide a basis for the design of new anticancer drugs, such as L-canavanine analogs.


  • Organizational Affiliation
    • Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 139.05 kDa 
  • Atom Count: 9,578 
  • Modeled Residue Count: 1,164 
  • Deposited Residue Count: 1,214 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginine--tRNA ligase, cytoplasmic
A, B
607Homo sapiensMutation(s): 1 
Gene Names: RARS
EC: 6.1.1.19
UniProt & NIH Common Fund Data Resources
Find proteins for P54136 (Homo sapiens)
Explore P54136 
Go to UniProtKB:  P54136
PHAROS:  P54136
GTEx:  ENSG00000113643 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54136
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.393α = 90
b = 109.31β = 90
c = 175.011γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description