3IRO

Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase complexed with NADPH and Q-8 antifolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.206 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural basis of antifolate inhibition of Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase

Chitnumsub, P.Yuvaniyama, J.Vilaivan, T.Vanichtanankul, J.Kamchonwongpaisan, S.Yuthavong, Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase
A, B, C, D
521Trypanosoma cruziMutation(s): 0 
EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for Q27793 (Trypanosoma cruzi)
Explore Q27793 
Go to UniProtKB:  Q27793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ27793
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
Q [auth C],
X [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
2CY
Query on 2CY

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
W [auth D]
5-[3-(3-fluorophenoxy)propoxy]quinazoline-2,4-diamine
C17 H17 F N4 O2
WYNJMQXBACXTGZ-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
R [auth C],
S [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
N [auth B],
T [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
H [auth A]
I [auth A]
J [auth A]
AA [auth D],
BA [auth D],
H [auth A],
I [auth A],
J [auth A],
O [auth B],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.544α = 90
b = 165.936β = 113.41
c = 84.718γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description