4N10 | pdb_00004n10

Crystal structure of plasmodium falciparum oxidized glutaredoxin 1 (PfGrx1) complexed with cisplatin

• PDB DOI: https://doi.org/10.2210/pdb4N10/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-03 Released: 2014-10-08 
• Deposition Author(s): Yogavel, M., Sharma, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.223 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

Interaction of Cisplatin with plasmodium falciparum Glutaredoxin 1

Yogavel, M., Tripathi, T., Rahlfs, S., Becker, K., Sharma, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 13.66 kDa 
• Atom Count: 1,039 
• Modelled Residue Count: 107 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutaredoxin	A	111	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: GRX1 EC: 1.20.4.1
UniProt
Find proteins for Q9NLB2 (Plasmodium falciparum (isolate 3D7)) Explore Q9NLB2  Go to UniProtKB:  Q9NLB2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPT	D [auth A], E [auth A], F [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
MPO	B [auth A]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N
MPD	C [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free:  0.223 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.652	α = 90
b = 48.652	β = 90
c = 83.234	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Yogavel, M., Sharma, A.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary