Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34959.92 
• Atom Count: 2568 
• Residue Count: 316 
• Unique protein chains: 1

3TQE

Structure of the malonyl CoA-acyl carrier protein transacylase (fabD) from Coxiella burnetii

• DOI: 10.2210/pdb3TQE/pdb

• Classification: TRANSFERASE
• Organism(s): Coxiella burnetii (strain RSA 493 / Nine Mile phase I)
• Expression System: Escherichia coli


• Deposited: 2011-09-09 Released: 2011-09-21 
• Deposition Author(s): Franklin, M.C., Cheung, J., Rudolph, M., Cassidy, M., Gary, E., Burshteyn, F., Love, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.171 
• R-Value Work: 0.146 

Literature

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

• PubMed: 26033498 
• DOI: 10.1002/prot.24841
• Primary Citation of Related Structures:  
  4NG4, 4NBQ, 4F3R, 4F3Q, 3UWC, 3TY2, 3TTH, 3TRI, 3TRH, 3TRG, 3TRF, 3TRE, 3TRD, 3TRC, 3TRB, 3TR9, 3TR8, 3TR7, 3TR6, 3TR5, 3TR4, 3TR3, 3TR2, 3TR1, 3TR0, 3TQZ, 3TQY, 3TQX, 3TQW, 3TQU, 3TQT, 3TQS, 3TQR, 3TQQ, 3TQP, 3TQO, 3TQN, 3TQM, 3TQL, 3TQJ,
  4NG4, 4NBQ, 4F3R, 4F3Q, 3UWC, 3TY2, 3TTH, 3TRI, 3TRH, 3TRG, 3TRF, 3TRE, 3TRD, 3TRC, 3TRB, 3TR9, 3TR8, 3TR7, 3TR6, 3TR5, 3TR4, 3TR3, 3TR2, 3TR1, 3TR0, 3TQZ, 3TQY, 3TQX, 3TQW, 3TQU, 3TQT, 3TQS, 3TQR, 3TQQ, 3TQP, 3TQO, 3TQN, 3TQM, 3TQL, 3TQJ, 3TQI, 3TQH, 3TQG, 3TQF, 3TQD, 3TQC, 3TQB, 3TQA, 3TQ9, 3TQ8


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Malonyl-CoA-[acyl-carrier-protein] transacylase	A	316	Coxiella burnetii (strain RSA 493 / Nine Mile phase I)	Mutation(s): 0  Gene Names: fabD EC: 2.3.1.39
Find proteins for Q83E39 (Coxiella burnetii (strain RSA 493 / Nine Mile phase I)) Go to UniProtKB:  Q83E39

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GLY	A	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.5 Å
• R-Value Free: 0.171 
• R-Value Work: 0.146 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 173.360	α = 90.00
b = 63.184	β = 98.81
c = 42.769	γ = 90.00

Software Package:

Software Name	Purpose
SOLVE	phasing
HKL-2000	data scaling
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-09 
• Released Date: 2011-09-21 
• Deposition Author(s): Franklin, M.C., Cheung, J., Rudolph, M., Cassidy, M., Gary, E., Burshteyn, F., Love, J.

Revision History 

• Version 1.0: 2011-09-21
  Type: Initial release
• Version 1.1: 2015-06-24
  Type: Database references
• Version 1.2: 2016-01-27
  Type: Database references