4PD8 | pdb_00004pd8

Structure of vcCNT-7C8C bound to pyrrolo-cytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.204 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters.

Johnson, Z.L.Lee, J.H.Lee, K.Lee, M.Kwon, D.Y.Hong, J.Lee, S.Y.

(2014) Elife 3: e03604-e03604

  • DOI: https://doi.org/10.7554/eLife.03604
  • Primary Citation Related Structures: 
    4PB1, 4PB2, 4PD5, 4PD6, 4PD7, 4PD8, 4PD9, 4PDA

  • PubMed Abstract: 

    Concentrative nucleoside transporters (CNTs) are responsible for cellular entry of nucleosides, which serve as precursors to nucleic acids and act as signaling molecules. CNTs also play a crucial role in the uptake of nucleoside-derived drugs, including anticancer and antiviral agents. Understanding how CNTs recognize and import their substrates could not only lead to a better understanding of nucleoside-related biological processes but also the design of nucleoside-derived drugs that can better reach their targets. Here, we present a combination of X-ray crystallographic and equilibrium-binding studies probing the molecular origins of nucleoside and nucleoside drug selectivity of a CNT from Vibrio cholerae. We then used this information in chemically modifying an anticancer drug so that it is better transported by and selective for a single human CNT subtype. This work provides proof of principle for utilizing transporter structural and functional information for the design of compounds that enter cells more efficiently and selectively.


  • Organizational Affiliation
    • Department of Biochemistry, Duke University Medical Center, Durham, United States.

Macromolecule Content 

  • Total Structure Weight: 44.94 kDa 
  • Atom Count: 2,978 
  • Modeled Residue Count: 404 
  • Deposited Residue Count: 424 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NupC family protein424Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 2 
Gene Names: VC_2352
Membrane Entity: Yes 
UniProt
Find proteins for Q9KPL5 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KPL5 
Go to UniProtKB:  Q9KPL5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KPL5
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.247 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.204 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.636α = 90
b = 119.636β = 90
c = 83.064γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM100984

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description