Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19148.43 
• Atom Count: 1342 
• Residue Count: 160 
• Unique protein chains: 1

4Q67

Staphylococcus aureus F98Y mutant dihydrofolate reductase complexed with NADPH

• DOI: 10.2210/pdb4Q67/pdb

• Classification: OXIDOREDUCTASE
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2014-04-21 Released: 2014-12-31 
• Deposition Author(s): Reeve, S.M., Anderson, A.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.233 
• R-Value Work: 0.175 

Literature

Protein design algorithms predict viable resistance to an experimental antifolate.

Reeve, S.M., Gainza, P., Frey, K.M., Georgiev, I., Donald, B.R., Anderson, A.C.

(2015) Proc.Natl.Acad.Sci.USA 112: 749-754

• PubMed: 25552560 
• DOI: 10.1073/pnas.1411548112
• Primary Citation of Related Structures:  
  4Q6A


• PubMed Abstract: 
  

Methods to accurately predict potential drug target mutations in response to early-stage leads could drive the design of more resilient first generation drug candidates. In this study, a structure-based protein design algorithm (K* in the OSPREY suite) was used to prospectively identify single-nucleotide polymorphisms that confer resistance to an experimental inhibitor effective against dihydrofolate reductase (DHFR) from Staphylococcus aureus. Four of the top-ranked mutations in DHFR were found to be catalytically competent and resistant to the inhibitor. Selection of resistant bacteria in vitro reveals that two of the predicted mutations arise in the background of a compensatory mutation. Using enzyme kinetics, microbiology, and crystal structures of the complexes, we determined the fitness of the mutant enzymes and strains, the structural basis of resistance, and the compensatory relationship of the mutations. To our knowledge, this work illustrates the first application of protein design algorithms to prospectively predict viable resistance mutations that arise in bacteria under antibiotic pressure.

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Organizational Affiliation: 

Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269; and.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Dihydrofolate reductase	A	160	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NAP	A	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.04 Å
• R-Value Free: 0.233 
• R-Value Work: 0.175 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 79.260	α = 90.00
b = 79.260	β = 90.00
c = 107.420	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
StructureStudio	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-04-21 
• Released Date: 2014-12-31 
• Deposition Author(s): Reeve, S.M., Anderson, A.C.

Revision History 

• Version 1.0: 2014-12-31
  Type: Initial release
• Version 1.1: 2015-02-18
  Type: Database references