3DMT

Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in complex with the irreversible iodoacetate inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Kinetic and Crystallographic Studies on Glyceraldehyde-3-Phosphate Dehydrogenase from Trypanosoma cruzi in Complex with Iodoacetate.

Guido, R.V.C.Balliano, T.L.Andricopulo, A.D.Oliva, G.

(2009) Letters In Drug Design & Discovery 6: 210-214


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase, glycosomalA, B, D359Trypanosoma cruziMutation(s): 0 
Gene Names: TcGAP
EC: 1.2.1.12
UniProt
Find proteins for P22513 (Trypanosoma cruzi)
Explore P22513 
Go to UniProtKB:  P22513
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenase, glycosomalC359Trypanosoma cruziMutation(s): 0 
Gene Names: TcGAP
EC: 1.2.1.12
UniProt
Find proteins for P22513 (Trypanosoma cruzi)
Explore P22513 
Go to UniProtKB:  P22513
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], I [auth D]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
CL-PEPTIDE LINKINGC5 H9 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.755α = 90
b = 83.713β = 96.44
c = 105.611γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description