3JW5

Crystal structure of Bacillus anthracis (Y102F) dihydrofolate reductase complexed with NADPH and Trimethoprim

• PDB DOI: https://doi.org/10.2210/pdb3JW5/pdb

• Classification: OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
• Organism(s): Bacillus anthracis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-09-17 Released: 2010-09-15 
• Deposition Author(s): Anderson, A.C., Beierlein, J.M., Karri, N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

Mutational Studies into Trimethoprim Resistance in Bacillus anthracis Dihydrofolate Reductase

Beierlein, J.M., Karri, N.G., 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.08 kDa 
• Atom Count: 2,940 
• Modelled Residue Count: 330 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	168	Bacillus anthracis	Mutation(s): 2  Gene Names: BAS2083, BA_2237, dfrA, GBAA2237, GBAA_2237 EC: 1.5.1.3
UniProt
Find proteins for Q81R22 (Bacillus anthracis) Explore Q81R22  Go to UniProtKB:  Q81R22

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], E [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TOP	D [auth A], F [auth B]	TRIMETHOPRIM C14 H18 N4 O3 IEDVJHCEMCRBQM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TOP	BindingDB:  3JW5	Ki: 2.41e+4 (nM) from 1 assay(s)
		IC50: min: 4.30e+4, max: 7.73e+4 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.260 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.991	α = 90
b = 74.991	β = 90
c = 67.41	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Anderson, A.C., Beierlein, J.M., Karri, N.G.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2013-11-20
  Changes: Non-polymer description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description