3S9U | pdb_00003s9u

Bacillus anthracis Dihydrofolate Reductase bound to propargyl-linked TMP analog, UCP120J

• PDB DOI: https://doi.org/10.2210/pdb3S9U/pdb

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


• Deposited: 2011-06-02 Released: 2012-06-13 
• Deposition Author(s): Anderson, A.C., Beierlein, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Structure-Activity Studies of Heterocyclic Propargyl-linked TMP Analogs Targeting Bacillus anthracis Dihydrofolate Reductase

Anderson, A.C., Beierlein, J.M., Viswanathan, K., Wright, D.L.

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: 41.42 kDa 
• Atom Count: 3,298 
• Modeled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrofolate reductase	A, B	165	Bacillus anthracis	Mutation(s): 1  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
NAP	C [auth A], E [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
5DR	D [auth A], F [auth B]	6-ethyl-5-[3-(4-methoxybiphenyl-3-yl)prop-1-yn-1-yl]pyrimidine-2,4-diamine C22 H22 N4 O LBQMRSNKEUNXMT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5DR	BindingDB:  3S9U	Ki: 1210 (nM) from 1 assay(s)
		IC50: 3600 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.187	α = 90
b = 78.187	β = 90
c = 67.094	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-13 
Deposition Author(s): Anderson, A.C., Beierlein, J.M.

Revision History  

• Version 1.0: 2012-06-13
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description