8EM8

Co-crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum in complex with RY-1-165

• PDB DOI: https://doi.org/10.2210/pdb8EM8/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-09-27 Released: 2022-11-02 
• Deposition Author(s): Hutchinson, A., Dong, A., Seitova, A., Bhanot, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.263 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Literature

Co-crystal structure of the cGMP-dependent protein kinase PKG from Plasmodium falciparum in complex with RY-1-165

Hutchinson, A., Dong, A., Seitova, A., Bhanot, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 98.63 kDa 
• Atom Count: 6,187 
• Modelled Residue Count: 783 
• Deposited Residue Count: 857 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cGMP-dependent protein kinase	A	853	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PKG, PF3D7_1436600 EC: 2.7.11.12
UniProt
Find proteins for Q8I719 (Plasmodium falciparum (isolate 3D7)) Explore Q8I719  Go to UniProtKB:  Q8I719

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
unidentified peptide fragment	B [auth U]	4	Plasmodium falciparum 3D7	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WLK (Subject of Investigation/LOI)	C [auth A]	[(3R)-3-{[(4M)-4-(4-cyclopropyl-2-phenyl-1H-imidazol-1-yl)pyrimidin-2-yl]amino}pyrrolidin-1-yl](1,3-thiazol-2-yl)methanone C24 H23 N7 O S WMOACOPVFVMARL-GOSISDBHSA-N
UNX	D [auth A], E [auth A], F [auth A], G [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.263 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M38EM8

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.145	α = 90
b = 127.986	β = 90
c = 213.728	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-02 
Deposition Author(s): Hutchinson, A., Dong, A., Seitova, A., Bhanot, P., Arrowsmith, C.H., Edwards, A.M., Halabelian, L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
Other private		--

Revision History  

• Version 1.0: 2022-11-02
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description