8D1W | pdb_00008d1w

Crystal structure of Plasmodium falciparum GRP78 in complex with (2R,3R,4S,5R)-2-(6-amino-8-((2-chlorobenzyl)amino)-9H-purin-9-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol

• PDB DOI: https://doi.org/10.2210/pdb8D1W/pdb

• Classification: CHAPERONE
• Organism(s): Plasmodium falciparum Palo Alto/Uganda
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-05-27 Released: 2023-05-31 
• Deposition Author(s): Mrozek, A., Chen, Y., Antoshchenko, T., Park, H.W., Smil, D., Zepeda, C.A.V.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Targeting Plasmodium falciparum GRP78: nucleoside analogues as agents against the malaria chaperone

Mrozek, A., Park, H.W.

(2022) Frontiers In Molecular Bioscience 

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: 44.96 kDa 
• Atom Count: 3,277 
• Modeled Residue Count: 377 
• Deposited Residue Count: 397 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone DnaK	A	397	Plasmodium falciparum Palo Alto/Uganda	Mutation(s): 0  Gene Names: PFUGPA_02944 EC: 3.6.4.10
UniProt
Find proteins for W4J0F1 (Plasmodium falciparum (isolate Palo Alto / Uganda)) Explore W4J0F1  Go to UniProtKB:  W4J0F1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HFY (Subject of Investigation/LOI)	B [auth A]	8-{[(2-chlorophenyl)methyl]amino}adenosine C17 H19 Cl N6 O4 HXRSLQGBEUJHPP-XNIJJKJLSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.288	α = 90
b = 84.288	β = 90
c = 292.218	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-31 
Deposition Author(s): Mrozek, A., Chen, Y., Antoshchenko, T., Park, H.W., Smil, D., Zepeda, C.A.V.

---

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-05-31
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description