5TBV | pdb_00005tbv

Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase complexed with tubercidin

• PDB DOI: https://doi.org/10.2210/pdb5TBV/pdb

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


• Deposited: 2016-09-13 Released: 2017-10-11 
• Deposition Author(s): Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP), Brazilian National Council for Scientific and Technological Development (CNPq)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Isoform 2 of Purine Nucleoside Phosphorylase

Torini, J.R., Romanello, L., Faheem, M., Bird, L., Owens, R., Brandao-Neto, J., Pereira, H.M.

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: 31.8 kDa 
• Atom Count: 2,328 
• Modeled 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBN	B [auth A]	'2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL C11 H14 N4 O4 HDZZVAMISRMYHH-KCGFPETGSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	D [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.981	α = 90
b = 91.981	β = 90
c = 91.981	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
xia2	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-11 
Deposition Author(s): Faheem, M., Torini, J.R., Romanello, L., Brandao-Neto, J., Pereira, H.M.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2012/14223-9
Brazilian National Council for Scientific and Technological Development (CNPq)	Brazil	474402/2013-4

Revision History  

• Version 1.0: 2017-10-11
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description