Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 146.46 kDa 
• Atom Count: 9961 
• Modelled Residue Count: 1089 
• Deposited Residue Count: 1216 
• Unique protein chains: 2

1J3J

Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with pyrimethamine, NADPH, and dUMP

• PDB DOI: 10.2210/pdb1J3J/pdb

• Classification: OXIDOREDUCTASE, TRANSFERASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-02-03 Released: 2003-05-06 
• Deposition Author(s): Yuvaniyama, J., Chitnumsub, P., Kamchonwongpaisan, S., Vanichtanankul, J., Sirawaraporn, W., Taylor, P., Walkinshaw, M., Yuthavong, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Insights into antifolate resistance from malarial DHFR-TS structures.

Yuvaniyama, J., Chitnumsub, P., Kamchonwongpaisan, S., Vanichtanankul, J., Sirawaraporn, W., Taylor, P., Walkinshaw, M.D., Yuthavong, Y.

(2003) Nat Struct Biol 10: 357-365

• PubMed: 12704428 
• DOI: 10.1038/nsb921
• Primary Citation of Related Structures:  
  1J3I, 1J3J, 1J3K


• PubMed Abstract: 
  

Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) is an important target of antimalarial drugs. The efficacy of this class of DHFR-inhibitor drugs is now compromised because of mutations that prevent drug binding yet retain enzyme activity. The crystal structures of PfDHFR-TS from the wild type (TM4/8.2) and the quadruple drug-resistant mutant (V1/S) strains, in complex with a potent inhibitor WR99210, as well as the resistant double mutant (K1 CB1) with the antimalarial pyrimethamine, reveal features for overcoming resistance. In contrast to pyrimethamine, the flexible side chain of WR99210 can adopt a conformation that fits well in the active site, thereby contributing to binding. The single-chain bifunctional PfDHFR-TS has a helical insert between the DHFR and TS domains that is involved in dimerization and domain organization. Moreover, positively charged grooves on the surface of the dimer suggest a function in channeling of substrate from TS to DHFR active sites. These features provide possible approaches for the design of new drugs to overcome antifolate resistance.

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Organizational Affiliation: 

Department of Biochemistry, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	A, B	280	Plasmodium falciparum	Mutation(s): 2  EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand)) Explore P13922  Go to UniProtKB:  P13922

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional dihydrofolate reductase-thymidylate synthase	C, D	328	Plasmodium falciparum	Mutation(s): 0  EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for P13922 (Plasmodium falciparum (isolate K1 / Thailand)) Explore P13922  Go to UniProtKB:  P13922

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	F [auth A], H [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
UMP	I [auth C], J [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N
CP6	E [auth A], G [auth B]	5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE C12 H13 Cl N4 WKSAUQYGYAYLPV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CP6	Binding MOAD:  1J3J	Ki: 9.8 (nM) from 1 assay(s)
	BindingDB:  1J3J	Ki: min: 0.19, max: 860 (nM) from 20 assay(s)
		IC50: min: 26, max: 1.00e+5 (nM) from 11 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.231 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.343	α = 90
b = 154.999	β = 90
c = 164.001	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
d*TREK	data reduction
d*TREK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-03 
• Released Date: 2003-05-06 
Deposition Author(s): Yuvaniyama, J., Chitnumsub, P., Kamchonwongpaisan, S., Vanichtanankul, J., Sirawaraporn, W., Taylor, P., Walkinshaw, M., Yuthavong, Y.

Revision History  

• Version 1.0: 2003-05-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations