7DIV

Structure of PfGrx1 in the intermediate state with cadmium

• PDB DOI: https://doi.org/10.2210/pdb7DIV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2020-11-19 Released: 2021-11-24 
• Deposition Author(s): Manickam, Y., Sharma, A.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.176 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Literature

Interaction of metals with PfGrx1

Manickam, Y., 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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 12.99 kDa 
• Atom Count: 1,003 
• 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: PF3D7_0306300 EC: 1.8.4.2
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
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
CD (Subject of Investigation/LOI)	D [auth A], E [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 0.176 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.198	α = 90
b = 48.198	β = 90
c = 82.721	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
Auto-Rickshaw	phasing
SHELXDE	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-24 
Deposition Author(s): Manickam, Y., Sharma, A.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2021-11-24
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Structure summary