6B6K

Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 6-methyl-2,3-dihydropyridazin-3-one

• PDB DOI: https://doi.org/10.2210/pdb6B6K/pdb

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


• Deposited: 2017-10-02 Released: 2018-10-10 
• Deposition Author(s): Faheem, M., Neto, J.B., Collins, P., Pearce, N.M., Valadares, N.F., Bird, L., Pereira, H.M., Delft, F.V., Barbosa, J.A.R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.184 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Starting Model: experimental

Literature

Crystal Structure of Purine Nucleoside Phosphorylase Isoform 2 from Schistosoma mansoni in complex with 3-methylpyridazin-1-ium-6-olate

Faheem, M., Neto, J.B., Collins, P., Pearce, N.M., Valadares, N.F., Bird, L., Pereira, H.M., Delft, F.V., Barbosa, J.A.R.G.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 32.09 kDa 
• Atom Count: 2,395 
• Modelled Residue Count: 283 
• Deposited Residue Count: 287 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A	287	Schistosoma mansoni	Mutation(s): 0  EC: 2.4.2.1
UniProt
Find proteins for A0A0U3AGT1 (Schistosoma mansoni) Explore A0A0U3AGT1  Go to UniProtKB:  A0A0U3AGT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CVG	I [auth A]	6-methylpyridazin-3-ol C5 H6 N2 O QZWIXLPWMGHDDD-UHFFFAOYSA-N
DMS	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.46 Å
• R-Value Free: 0.184 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.7	α = 90
b = 99.7	β = 90
c = 99.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XDS	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-10 
Deposition Author(s): Faheem, M., Neto, J.B., Collins, P., Pearce, N.M., Valadares, N.F., Bird, L., Pereira, H.M., Delft, F.V., Barbosa, J.A.R.G.

Revision History  

• Version 1.0: 2018-10-10
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.2: 2024-11-20
  Changes: Structure summary