6R1N | pdb_00006r1n

Crystal structure of S. aureus seryl-tRNA synthetase complexed to seryl sulfamoyl adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6R1N

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase.

Cain, R.Salimraj, R.Punekar, A.S.Bellini, D.Fishwick, C.W.G.Czaplewski, L.Scott, D.J.Harris, G.Dowson, C.G.Lloyd, A.J.Roper, D.I.

(2019) J Med Chem 62: 9703-9717

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01131
  • Primary Citation Related Structures: 
    6R1M, 6R1N, 6R1O

  • PubMed Abstract: 

    Aminoacyl-tRNA synthetases are ubiquitous and essential enzymes for protein synthesis and also a variety of other metabolic processes, especially in bacterial species. Bacterial aminoacyl-tRNA synthetases represent attractive and validated targets for antimicrobial drug discovery if issues of prokaryotic versus eukaryotic selectivity and antibiotic resistance generation can be addressed. We have determined high-resolution X-ray crystal structures of the Escherichia coli and Staphylococcus aureus seryl-tRNA synthetases in complex with aminoacyl adenylate analogues and applied a structure-based drug discovery approach to explore and identify a series of small molecule inhibitors that selectively inhibit bacterial seryl-tRNA synthetases with greater than 2 orders of magnitude compared to their human homologue, demonstrating a route to the selective chemical inhibition of these bacterial targets.


  • Organizational Affiliation
    • School of Life Sciences , University of Warwick , Gibbet Hill Road , Coventry CV4 7AL , United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 51.98 kDa 
  • Atom Count: 3,777 
  • Modeled Residue Count: 420 
  • Deposited Residue Count: 449 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine--tRNA ligase449Staphylococcus aureusMutation(s): 0 
Gene Names: 
EC: 6.1.1.11
UniProt
Find proteins for P95689 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P95689 
Go to UniProtKB:  P95689
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95689
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SSA
(Subject of Investigation/LOI)

Query on SSA



Download:Ideal Coordinates CCD File
B [auth A]5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A],
F [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.438α = 90
b = 116.413β = 90
c = 91.611γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M017893/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2021-02-10
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description