1J3J

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

Structural Biology Knowledgebase: 1J3J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.198

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1J3J

Classification: OXIDOREDUCTASE TRANSFERASE

Total Structure Weight: 146460.25

Macromolecule Entities
Molecule Chains Length Organism Details
Bifunctional dihydrofolate reductase-thymidylate synthase A, B 280 Plasmodium falciparum EC#: 1.5.1.3 IUBMB 2.1.1.45 IUBMB
Fragment: RESIDUES 1-280
Mutation: C59R, S108N
Gene Name(s):
Bifunctional dihydrofolate reductase-thymidylate synthase C, D 328 Plasmodium falciparum EC#: 1.5.1.3 IUBMB 2.1.1.45 IUBMB
Fragment: RESIDUES 281-608
Gene Name(s):

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NDP
Query on NDP

A, B NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UMP
Query on UMP

C, D 2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP (Synonym)
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CP6
Query on CP6

A, B 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4- DIAMINE
PYRIMETHAMINE (Synonym)
C12 H13 Cl N4
WKSAUQYGYAYLPV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
CP6 IC50: 80 - >100000 nM (99 - 100) BindingDB
Ki: 0.19 - 860 nM (99 - 100) BindingDB

Ki: 9.8 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.198
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.34 α = 90.00
b = 155.00 β = 90.00
c = 164.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



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

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4