2AM1

sp protein ligand 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of MurF from Streptococcus pneumoniae co-crystallized with a small molecule inhibitor exhibits interdomain closure

Longenecker, K.L.Stamper, G.F.Hajduk, P.J.Fry, E.H.Jakob, C.G.Harlan, J.E.Edalji, R.Bartley, D.M.Walter, K.A.Solomon, L.R.Holzman, T.F.Gu, Y.G.Lerner, C.G.Beutel, B.A.Stoll, V.S.

(2005) Protein Sci. 14: 3039-3047

  • DOI: 10.1110/ps.051604805
  • Primary Citation of Related Structures:  2AM2

  • PubMed Abstract: 
  • In a broad genomics analysis to find novel protein targets for antibiotic discovery, MurF was identified as an essential gene product for Streptococcus pneumonia that catalyzes a critical reaction in the biosynthesis of the peptidoglycan in the forma ...

    In a broad genomics analysis to find novel protein targets for antibiotic discovery, MurF was identified as an essential gene product for Streptococcus pneumonia that catalyzes a critical reaction in the biosynthesis of the peptidoglycan in the formation of the cell wall. Lacking close relatives in mammalian biology, MurF presents attractive characteristics as a potential drug target. Initial screening of the Abbott small-molecule compound collection identified several compounds for further validation as pharmaceutical leads. Here we report the integrated efforts of NMR and X-ray crystallography, which reveal the multidomain structure of a MurF-inhibitor complex in a compact conformation that differs dramatically from related structures. The lead molecule is bound in the substrate-binding region and induces domain closure, suggestive of the domain arrangement for the as yet unobserved transition state conformation for MurF enzymes. The results form a basis for directed optimization of the compound lead by structure-based design to explore the suitability of MurF as a pharmaceutical target.


    Organizational Affiliation

    Department of Structural Biology, R46Y, Building AP10, 100 Abbott Park Road, Abbott Park, IL 60064, USA. Kenton.Longenecker@Abbott.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylmuramoylalanine-D-glutamyl-lysine-D-alanyl-D-alanine ligase, MurF protein
A
454Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Gene Names: murF
EC: 6.3.2.10
Find proteins for Q8DNV6 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DNV6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
1LG
Query on 1LG

Download SDF File 
Download CCD File 
A
2,4-DICHLORO-N-(3-CYANO-4,5,6,7-TETRAHYDRO-BENZOTHIOPHEN-2YL)-5-(MORPHOLINE-4-SULFONYL)-BENZAMIDE
C20 H19 Cl2 N3 O4 S2
JMCVGASJAJMFPN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1LGIC50: 1000 nM (99) BINDINGDB
1LGIC50: 1000 nM BINDINGMOAD
1LGIC50: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 116.271α = 90.00
b = 116.271β = 90.00
c = 161.389γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CCP4data scaling
PDB_EXTRACTdata extraction
SOLVEphasing
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description