3IDS | pdb_00003ids

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

• PDB DOI: https://doi.org/10.2210/pdb3IDS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-21 Released: 2009-08-11 
• Deposition Author(s): Balliano, T.L., Guido, R.V.C., Andricopulo, A.D., Oliva, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

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

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 157.84 kDa 
• Atom Count: 12,142 
• Modeled Residue Count: 1,436 
• Deposited Residue Count: 1,436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde-3-phosphate dehydrogenase, glycosomal	A [auth C], B [auth D], C [auth A], D [auth B]	359	Trypanosoma cruzi	Mutation(s): 0  EC: 1.2.1.12
UniProt
Find proteins for P22513 (Trypanosoma cruzi) Explore P22513  Go to UniProtKB:  P22513

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	G [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GOL	F [auth C], H [auth D], I [auth D], K [auth A], L [auth A], N [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACM	E [auth C], J [auth A], M [auth B]	ACETAMIDE C2 H5 N O DLFVBJFMPXGRIB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.121	α = 90
b = 85.388	β = 96.42
c = 105.66	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Balliano, T.L., Guido, R.V.C., Andricopulo, A.D., Oliva, G.

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description