3QGT

Crystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dUMP AND PYRIMETHAMINE

Structural Biology Knowledgebase: 3QGT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QGT

Classification: OXIDOREDUCTASE TRANSFERASE / INHIBITOR

Total Structure Weight: 146261.97

Macromolecule Entities
Molecule Chains Length Organism Details
Bifunctional dihydrofolate reductase-thymidylate synthase A, B 608 Plasmodium falciparum EC#: 1.5.1.3 IUBMB 2.1.1.45 IUBMB
Gene Name(s): DHFR-TS dhfr-ts
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 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) BindingDB
Ki: 0.19 - 860 nM (99 - 100) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.222
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.10 α = 90.00
b = 154.44 β = 90.00
c = 164.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-24
  • Released Date: 2011-06-29
  • Deposition author(s): Chitnumsub, P., Yuthavong, Y.

Revision History

  • 2014-11-12
    Type: Function and keywords | Details: --
  • 2013-06-26
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4