Crystal structure of ArnB aminotransferase with cycloserine and pyridoxal 5' phosphate

Experimental Data Snapshot

  • Resolution: 2.07 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.223 

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Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: A 4-amino-4-deoxy-L-arabinose lipopolysaccharide modifying enzyme

Noland, B.W.Newman, J.M.Hendle, J.Badger, J.Christopher, J.A.Tresser, J.Buchanan, M.D.Wright, T.Rutter, M.E.Sanderson, W.E.Muller-Dieckmann, H.-J.Gajiwala, K.Buchanan, S.G.

(2002) Structure 10: 1569-1580

  • DOI: https://doi.org/10.1016/s0969-2126(02)00879-1
  • Primary Citation of Related Structures:  
    1MDO, 1MDX, 1MDZ

  • PubMed Abstract: 

    Lipid A modification with 4-amino-4-deoxy-L-arabinose confers on certain pathogenic bacteria, such as Salmonella, resistance to cationic antimicrobial peptides, including those derived from the innate immune system. ArnB catalysis of amino group transfer from glutamic acid to the 4"-position of a UDP-linked ketopyranose molecule to form UDP-4-amino-4-deoxy-L-arabinose represents a key step in the lipid A modification pathway. Structural and functional studies of the ArnB aminotransferase were undertaken by combining X-ray crystallography with biochemical analyses. High-resolution crystal structures were solved for two native forms and one covalently inhibited form of S. typhimurium ArnB. These structures permitted identification of key residues involved in substrate binding and catalysis, including a rarely observed nonprolyl cis peptide bond in the active site.

  • Organizational Affiliation

    Structural Genomix, San Diego, CA 92121, USA. brian.noland@stromix.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ArnB aminotransferase393Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Find proteins for Q8ZNF3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q8ZNF3 
Go to UniProtKB:  Q8ZNF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ZNF3
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DCS

Download Ideal Coordinates CCD File 
C11 H16 N3 O7 P
Query on PLP

Download Ideal Coordinates CCD File 
C8 H10 N O6 P
Experimental Data & Validation

Experimental Data

  • Resolution: 2.07 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.223 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.904α = 90
b = 90.904β = 90
c = 127.71γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-11
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Advisory, Data collection
  • Version 1.4: 2018-10-10
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.5: 2018-12-26
    Changes: Data collection, Structure summary