5JBQ | pdb_00005jbq

EF-TU (ESCHERICHIA COLI) IN COMPLEX WITH THIOMURACIN ANALOG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.253 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.204 (Depositor) 
  • R-Value Observed: 
    0.207 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5JBQ

Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 

Literature

Antibacterial and Solubility Optimization of Thiomuracin A.

LaMarche, M.J., Leeds, J.A., Brewer, J., Dean, K., Ding, J., Dzink-Fox, J., Gamber, G., Jain, A., Kerrigan, R., Krastel, P., Lee, K., Lombardo, F., McKenney, D., Neckermann, G., Osborne, C., Palestrant, D., Patane, M.A., Rann, E.M., Robinson, Z., Schmitt, E., Stams, T., Tiamfook, S., Yu, D., Whitehead, L.

(2016) J Med Chem 59: 6920-6928

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00726
  • Primary Citation Related Structures: 
    5JBQ

  • PubMed Abstract: 

    Synthetic studies of the antimicrobial secondary metabolite thiomuracin A (1) provided access to analogues in the Northern region (C2-C10). Selective hydrolysis of the C10 amide of lead compound 2 and subsequent derivatization led to novel carbon- and nitrogen-linked analogues (e.g., 3) which improved antibacterial potency across a panel of Gram-positive organisms. In addition, congeners with improved physicochemical properties were identified which proved efficacious in murine sepsis and hamster C. difficile models of disease. Optimal efficacy in the hamster model of C. difficile was achieved with compounds that possessed both potent antibacterial activity and high aqueous solubility.

    • Organizational Affiliation: 
    • Infectious Disease Area, Novartis Institutes for Biomedical Research , Emeryville, California 94608, United States.

Macromolecule Content 

  • Total Structure Weight: 45.43 kDa 
  • Atom Count: 3,376 
  • Modeled Residue Count: 405 
  • Deposited Residue Count: 407 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor Tu 1394Escherichia coli K-12Mutation(s): 0 
Gene Names: tufA, b3339, JW3301
EC: 3.6.5.3
UniProt
Find proteins for P0CE47 (Escherichia coli (strain K12))
Explore P0CE47 
Go to UniProtKB:  P0CE47
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CE47
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
THIOMURACIN ANALOG13synthetic constructMutation(s): 0 

Small Molecules

Modified Residues  5 Unique
IDChains TypeFormula2D DiagramParent
05N
Query on 05N
B
L-PEPTIDE LINKINGC6 H11 N O3PRO
6RK
Query on 6RK
B
L-PEPTIDE LINKINGC7 H13 N O2

--

BB6
Query on BB6
B
PEPTIDE LINKINGC4 H7 N O2 SCYS
BB9
Query on BB9
B
PEPTIDE LINKINGC3 H5 N O2 SCYS
H14
Query on H14
B
L-PEPTIDE LINKINGC9 H11 N O3PHE
MH6
Query on MH6
B
PEPTIDE LINKINGC3 H5 N O3SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.253 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.204 (Depositor) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.35α = 90
b = 125.34β = 90
c = 45.4γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary