Structure of the dihydrofolate reductase (folA) from Coxiella burnetii in complex with trimethoprim

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.4 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
Dihydrofolate reductase178Coxiella burnetiiMutation(s): 0 
Gene Names: CBU_1993folA
Find proteins for Q83AB2 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I))
Explore Q83AB2 
Go to UniProtKB:  Q83AB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83AB2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NDP

Download Ideal Coordinates CCD File 
C21 H30 N7 O17 P3
Query on TOP

Download Ideal Coordinates CCD File 
C14 H18 N4 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 36.2β = 110.27
c = 53.81γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2015-06-24
    Changes: Database references
  • Version 1.2: 2016-01-20
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description