3DG8

Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with RJF670, NADPH, and dUMP

Structural Biology Knowledgebase: 3DG8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.199

Literature

Macromolecules
Sequence Display for 3DG8

Classification: OXIDOREDUCTASE TRANSFERASE

Total Structure Weight: 146435.52

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: N51I, C59R, S108N, I164L
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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 NGL
 
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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RJ6
Query on RJ6

A, B N-(3,5-dimethoxyphenyl)imidodicarbonimidic diamide
{[(3,5-dimethoxyanilino)(imino)methyl]amino}methanimidamide (Synonym)
C10 H15 N5 O2
VQKIGKHIRBCYNE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RJ6 N/A in BindingDB
N/A in BindingMoad
IC50: 20000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.199
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.52 α = 90.00
b = 155.40 β = 90.00
c = 165.18 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