2W3A

HUMAN DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM

• PDB DOI: https://doi.org/10.2210/pdb2W3A/pdb

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


• Deposited: 2008-11-10 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: 1.50 Å
• R-Value Free: 0.214 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 

Starting Model: other

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)

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: 45.31 kDa 
• Atom Count: 3,650 
• Modelled Residue Count: 372 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROFOLATE REDUCTASE	A, B	187	Homo sapiens	Mutation(s): 0  EC: 1.5.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00374 (Homo sapiens) Explore P00374  Go to UniProtKB:  P00374
PHAROS:  P00374 GTEx:  ENSG00000228716

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	D [auth A], H [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
TOP	F [auth A], I [auth B]	TRIMETHOPRIM C14 H18 N4 O3 IEDVJHCEMCRBQM-UHFFFAOYSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TOP	BindingDB:  2W3A	Ki: min: 6.00e-3, max: 10 (nM) from 2 assay(s)
		IC50: min: 27, max: 2.60e+5 (nM) from 31 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.214 
• R-Value Work: 0.179 
• R-Value Observed: 0.181 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.468	α = 90
b = 94.014	β = 90
c = 96.576	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: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.5: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description