Structure of phosphoglycerate kinase (CBU_1782) from Coxiella burnetii

Experimental Data Snapshot

  • Resolution: 2.78 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.274 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Structural genomics for drug design against the pathogen Coxiella burnetii.

Franklin, M.C.Cheung, J.Rudolph, M.J.Burshteyn, F.Cassidy, M.Gary, E.Hillerich, B.Yao, Z.K.Carlier, P.R.Totrov, M.Love, J.D.

(2015) Proteins 83: 2124-2136

  • DOI: https://doi.org/10.1002/prot.24841
  • Primary Citation of Related Structures:  
    3TQ8, 3TQ9, 3TQA, 3TQB, 3TQC, 3TQD, 3TQE, 3TQF, 3TQG, 3TQH, 3TQI, 3TQJ, 3TQL, 3TQM, 3TQN, 3TQO, 3TQP, 3TQQ, 3TQR, 3TQS, 3TQT, 3TQU, 3TQW, 3TQX, 3TQY, 3TQZ, 3TR0, 3TR1, 3TR2, 3TR3, 3TR4, 3TR5, 3TR6, 3TR7, 3TR8, 3TR9, 3TRB, 3TRC, 3TRD, 3TRE, 3TRF, 3TRG, 3TRH, 3TRI, 3TTH, 3TY2, 3UWC, 4F3Q, 4F3R, 4NBQ

  • PubMed Abstract: 

    Coxiella burnetii is a highly infectious bacterium and potential agent of bioterrorism. However, it has not been studied as extensively as other biological agents, and very few of its proteins have been structurally characterized. To address this situation, we undertook a study of critical metabolic enzymes in C. burnetii that have great potential as drug targets. We used high-throughput techniques to produce novel crystal structures of 48 of these proteins. We selected one protein, C. burnetii dihydrofolate reductase (CbDHFR), for additional work to demonstrate the value of these structures for structure-based drug design. This enzyme's structure reveals a feature in the substrate binding groove that is different between CbDHFR and human dihydrofolate reductase (hDHFR). We then identified a compound by in silico screening that exploits this binding groove difference, and demonstrated that this compound inhibits CbDHFR with at least 25-fold greater potency than hDHFR. Since this binding groove feature is shared by many other prokaryotes, the compound identified could form the basis of a novel antibacterial agent effective against a broad spectrum of pathogenic bacteria.

  • Organizational Affiliation

    Special Projects Division, New York Structural Biology Center, New York.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphoglycerate kinase
A, B, C
404Coxiella burnetii RSA 493Mutation(s): 0 
Gene Names: CBU_1782pgk
Find proteins for Q83AU6 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I))
Explore Q83AU6 
Go to UniProtKB:  Q83AU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83AU6
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.78 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.272 
  • R-Value Observed: 0.274 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.148α = 90
b = 91.568β = 102.17
c = 88.412γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-24
    Type: Initial release
  • Version 1.1: 2016-01-27
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description