2QAE | pdb_00002qae

Crystal Structure Analysis of Trypanosoma cruzi Lipoamide dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb2QAE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-06-15 Released: 2008-07-22 
• Deposition Author(s): Werner, C., Krauth-Siegel, R.L., Stubbs, M.T., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of lipoamide dehydrogenase from Trypanosoma cruzi: A Putative target for the design of new drugs against Chagas disease

Werner, C., Krauth-Siegel, R.L., Stubbs, M.T., Klebe, G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 100.5 kDa 
• Atom Count: 7,134 
• Modeled Residue Count: 930 
• Deposited Residue Count: 936 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B	468	Trypanosoma cruzi	Mutation(s): 5  Gene Names: LPD EC: 1.8.1.4
UniProt
Find proteins for P90597 (Trypanosoma cruzi) Explore P90597  Go to UniProtKB:  P90597

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.187 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.7	α = 90
b = 104.9	β = 90
c = 147.4	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-22 
Deposition Author(s): Werner, C., Krauth-Siegel, R.L., Stubbs, M.T., Klebe, G.

Revision History  

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary