3DGA

Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with RJF01302, NADPH, and dUMP

Structural Biology Knowledgebase: 3DGA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3DGA

Classification: OXIDOREDUCTASE TRANSFERASE

Total Structure Weight: 146359.92

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
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)
RJ1
Query on RJ1

A, B N-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide
2-{[{[amino(imino)methyl]amino}(imino)methyl]amino}- 1-chloro-4-(trifluoromethyl)benzene (Synonym)
C9 H9 Cl F3 N5
IGFTZEOFHWPCDL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RJ1 N/A in BindingDB
N/A in BindingMoad
IC50: 29900 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.205
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.38 α = 90.00
b = 156.01 β = 90.00
c = 164.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-13
  • Released Date: 2009-01-27
  • Deposition author(s): Dasgupta, T., Chitnumsub, P., Maneeruttanarungroj, C., Kamchonwongpaisan, S., Nichols, S., Lyons, T.M., Tirado-Rives, J., Jorgensen, W.L., Yuthavong, Y., Anderson, K.S.

Revision History

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