5JNQ

MraY tunicamycin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

MraY-antibiotic complex reveals details of tunicamycin mode of action.

Hakulinen, J.K.Hering, J.Branden, G.Chen, H.Snijder, A.Ek, M.Johansson, P.

(2017) Nat Chem Biol 13: 265-267

  • DOI: 10.1038/nchembio.2270
  • Primary Citation of Related Structures:  
    5JNQ

  • PubMed Abstract: 
  • The rapid increase of antibiotic resistance has created an urgent need to develop novel antimicrobial agents. Here we describe the crystal structure of the promising bacterial target phospho-N-acetylmuramoyl-pentapeptide translocase (MraY) in complex ...

    The rapid increase of antibiotic resistance has created an urgent need to develop novel antimicrobial agents. Here we describe the crystal structure of the promising bacterial target phospho-N-acetylmuramoyl-pentapeptide translocase (MraY) in complex with the nucleoside antibiotic tunicamycin. The structure not only reveals the mode of action of several related natural-product antibiotics but also gives an indication on the binding mode of the MraY UDP-MurNAc-pentapeptide and undecaprenyl-phosphate substrates.


    Organizational Affiliation

    Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D Gothenburg, Gothenburg, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospho-N-acetylmuramoyl-pentapeptide-transferaseA376[Clostridium] bolteae 90A9Mutation(s): 0 
Gene Names: mraYHMPREF1085_00623
EC: 2.7.8.13
Find proteins for R0BTE9 ([Clostridium] bolteae 90A9)
Explore R0BTE9 
Go to UniProtKB:  R0BTE9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TUM
Query on TUM

Download CCD File 
A
Tunicamycin
C37 H60 N4 O16
YJQCOFNZVFGCAF-DCSBULBVSA-N
 Ligand Interaction
BOG
Query on BOG

Download CCD File 
A
octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
PLM
Query on PLM

Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.64α = 90
b = 105.54β = 90
c = 134.96γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2016-04-30 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Johansson, P.

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2017-02-22
    Changes: Database references
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary