3PHC | pdb_00003phc

Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG

• PDB DOI: https://doi.org/10.2210/pdb3PHC/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-11-03 Released: 2011-11-09 
• Deposition Author(s): Ho, M., Edwards, A.A., Almo, S.C., Schramm, V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal Structure of Plasmodium falciparum purine nucleoside phosphorylase in complex with DADMe-ImmG

Ho, M., Edwards, A.A., Almo, S.C., Schramm, V.L.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 184.95 kDa 
• Atom Count: 11,631 
• Modeled Residue Count: 1,458 
• Deposited Residue Count: 1,650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A, B, C, D, E, F	275	Plasmodium falciparum	Mutation(s): 0  Gene Names: PNP EC: 2.4.2.1 (PDB Primary Data), 2.4.2.44 (UniProt)
UniProt
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7)) Explore Q8I3X4  Go to UniProtKB:  Q8I3X4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IM5	I [auth A], K [auth B], N [auth C], P [auth D], S [auth E], U [auth F]	2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one C12 H17 N5 O3 GSPTUGDLYPMLCQ-SFYZADRCSA-N
PO4	H [auth A], J [auth B], M [auth C], O [auth D], R [auth E], T [auth F]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	G [auth A], L [auth C], Q [auth E]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IM5	BindingDB:  3PHC	Ki: min: 0.89, max: 890 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.197	α = 67.71
b = 77.371	β = 73.62
c = 92.197	γ = 86.03

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-09 
Deposition Author(s): Ho, M., Edwards, A.A., Almo, S.C., Schramm, V.L.

Revision History  

• Version 1.0: 2011-11-09
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations