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), 0.212 (DCC)
R-Value Work:
0.190 (Depositor)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Mrozek, A., Park, H.W.

(2022) Frontiers In Molecular Bioscience

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W4J0F1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HFY (Subject of Investigation/LOI) Query on HFY Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	8-{[(2-chlorophenyl)methyl]amino}adenosine C₁₇ H₁₉ Cl N₆ O₄ HXRSLQGBEUJHPP-XNIJJKJLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.221 (Depositor), 0.212 (DCC)
R-Value Work: 0.190 (Depositor)
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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-31

Deposition Author(s):

Antoshchenko, T.

Funding Organization	Location	Grant Number
Other private	United States	--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.