2W3V

MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM

• PDB DOI: https://doi.org/10.2210/pdb2W3V/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium avium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-11-16 Released: 2009-11-17 
• Deposition Author(s): Leung, A.K.W., Reynolds, R.C., Borhani, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Model: experimental

Literature

Structural Basis for Selective Inhibition of Mycobacterium Avium Dihydrofolate Reductase by a Lipophilic Antifolate

Leung, A.K.W., Ross, L.J., Zywno-Van Ginkel, S., Reynolds, R.C., Seitz, L.E., Pathak, V., Barrow, W.W., White, E.L., Suling, W.J., Piper, J.R., Borhani, D.W.

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: 19.49 kDa 
• Atom Count: 1,545 
• Modelled Residue Count: 165 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROFOLATE REDUCTASE	A	167	Mycobacterium avium	Mutation(s): 0  EC: 1.5.1.3
UniProt
Find proteins for O30463 (Mycobacterium avium) Explore O30463  Go to UniProtKB:  O30463

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
TOP	BindingDB:  2W3V	IC50: min: 190, max: 5750 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.816	α = 90
b = 70.816	β = 90
c = 73.613	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Leung, A.K.W., Reynolds, R.C., Borhani, D.W.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-04-11
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2019-03-06
  Changes: Data collection, Derived calculations, Experimental preparation
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description