3PHC

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Purine nucleoside phosphorylase
A, B, C, D, E, F
A, B, C, D, E, F
275Plasmodium falciparumMutation(s): 0 
Gene Names: PNP
EC: 2.4.2.1
UniProt
Find proteins for Q8I3X4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I3X4 
Go to UniProtKB:  Q8I3X4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I3X4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IM5
Query on IM5

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
N [auth C],
P [auth D],
S [auth E],
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
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B],
M [auth C],
O [auth D],
R [auth E],
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
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
G [auth A],
L [auth C],
Q [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.197α = 67.71
b = 77.371β = 73.62
c = 92.197γ = 86.03
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description