1JIL

Crystal structure of S. aureus TyrRS in complex with SB284485


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystal structure of Staphylococcus aureus tyrosyl-tRNA synthetase in complex with a class of potent and specific inhibitors.

Qiu, X.Janson, C.A.Smith, W.W.Green, S.M.McDevitt, P.Johanson, K.Carter, P.Hibbs, M.Lewis, C.Chalker, A.Fosberry, A.Lalonde, J.Berge, J.Brown, P.Houge-Frydrych, C.S.Jarvest, R.L.

(2001) Protein Sci 10: 2008-2016

  • DOI: https://doi.org/10.1110/ps.18001
  • Primary Citation of Related Structures:  
    1JII, 1JIJ, 1JIK, 1JIL

  • PubMed Abstract: 

    SB-219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl-tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl-tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital-acquired infections. The full-length enzyme yielded crystals that diffracted to 2.8 A resolution, but a truncated version of the enzyme allowed the resolution to be extended to 2.2 A. These inhibitors not only occupy the known substrate binding sites in unique ways, but also reveal a butyl binding pocket. It was reported that the Bacillus stearothermophilus TyrRS T51P mutant has much increased catalytic activity. The S. aureus enzyme happens to have a proline at position 51. Therefore, our structures may contribute to the understanding of the catalytic mechanism and provide the structural basis for designing novel antimicrobial agents.


  • Organizational Affiliation

    GlaxoSmithKline, King of Prussia, Pennsylvania 19406, USA. xiayang_qui-1@sbphrd.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tyrosyl-tRNA synthetase420Staphylococcus aureusMutation(s): 0 
EC: 6.1.1.1
UniProt
Find proteins for A6QHR2 (Staphylococcus aureus (strain Newman))
Explore A6QHR2 
Go to UniProtKB:  A6QHR2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6QHR2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
485
Query on 485

Download Ideal Coordinates CCD File 
B [auth A][2-AMINO-3-(4-HYDROXY-PHENYL)-PROPIONYLAMINO]- (3,4,5-TRIHYDROXY-6-METHYL-TETRAHYDRO-PYRAN-2-YL)- ACETIC ACID
C17 H24 N2 O8
KUCHJUZRDGYEDY-HRNUQJICSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
485 PDBBind:  1JIL IC50: 4 (nM) from 1 assay(s)
BindingDB:  1JIL IC50: 4 (nM) from 1 assay(s)
Binding MOAD:  1JIL IC50: 4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.183 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66α = 90
b = 102.9β = 90
c = 139.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-10-26
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description