3F0S

Staphylococcus aureus dihydrofolate reductase complexed with NADPH and 2,4-Diamino-5-[3-(3-methoxy-5-(3,5-dimethylphenyl)phenyl)but-1-ynyl]-6-methylpyrimidine

• PDB DOI: https://doi.org/10.2210/pdb3F0S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Staphylococcus aureus RF122
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-25 Released: 2009-10-06 
• Deposition Author(s): Anderson, A.C., Frey, K.M., Liu, J., Lombardo, M.N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: other

Literature

Crystallographic Complexes of Wildtype and Mutant MRSA DHFR Reveal Interactions for Lead Design

Frey, K.M., Liu, J., Lombardo, M.N., Bolstad, D.B., Smith, A.E., Priestley, N.D., Wright, D.L., Anderson, A.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 19.15 kDa 
• Atom Count: 1,350 
• Modelled Residue Count: 157 
• Deposited Residue Count: 157 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trimethoprim-sensitive dihydrofolate reductase	A [auth X]	157	Staphylococcus aureus RF122	Mutation(s): 0  Gene Names: dfrB EC: 1.5.1.3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	B [auth X]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
53T	C [auth X]	5-[(3R)-3-(5-methoxy-3',5'-dimethylbiphenyl-3-yl)but-1-yn-1-yl]-6-methylpyrimidine-2,4-diamine C24 H26 N4 O ATFDKOLABYIYCC-INIZCTEOSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
53T	BindingDB:  3F0S	IC50: 42 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.958	α = 90
b = 78.958	β = 90
c = 107.422	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Anderson, A.C., Frey, K.M., Liu, J., Lombardo, M.N.

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-11-27
  Changes: Non-polymer description
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-04-03
  Changes: Refinement description