4CP5 | pdb_00004cp5

ndpK in complex with (Rp)-SPMPApp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free: 
    0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.201 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Enzymatic Synthesis of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect of the Alpha-Phosphorus Configuration on HIV-1 RT Activity.

Priet, S.Roux, L.Saez-Ayala, M.Ferron, F.Canard, B.Alvarez, K.

(2015) Antiviral Res 117: 122

  • DOI: https://doi.org/10.1016/j.antiviral.2015.03.003
  • Primary Citation Related Structures: 
    4C6A, 4CP5

  • PubMed Abstract: 

    The acyclic nucleosides thiophosphonates (9-[2-(thiophosphonomethoxy)ethyl]adenine (S-PMEA) and (R)-9-[2-(thiophosphonomethoxy)propyl]adenine (S-PMPA), exhibit antiviral activity against HIV-1, -2 and HBV. Their diphosphate forms S-PMEApp and S-PMPApp, synthesized as stereoisomeric mixture, are potent inhibitors of wild-type (WT) HIV-1 RT. Understanding HIV-1 RT stereoselectivity, however, awaits resolution of the diphosphate forms into defined stereoisomers. To this aim, thiophosphonate monophosphates S-PMEAp and S-PMPAp were synthesized and used in a stereocontrolled enzyme-catalyzed phosphoryl transfer reaction involving either nucleoside diphosphate kinase (NDPK) or creatine kinase (CK) to obtain thiophosphonate diphosphates as separated isomers. We then quantified substrate preference of recombinant WT HIV-1 RT toward pure stereoisomers using in vitro steady-state kinetic analyses. The crystal structure of a complex between Dictyostelium NDPK and S-PMPApp at 2.32Å allowed to determine the absolute configuration at the α-phosphorus atom in relation to the stereo-preference of studied enzymes. The RP isomer of S-PMPApp and S-PMEApp are the preferred substrate over SP for both NDPK and HIV-1 RT.


  • Organizational Affiliation
    • Laboratoire d'Architecture et Fonction des Macromolécules Biologiques, UMR CNRS 7257, Team "Viral Replicases: Structure, Mechanism and Drug-Design", Université Aix-Marseille, Parc scientifique de Luminy, 163 av. de Luminy, 13288 Marseille Cedex 9, France.

Macromolecule Content 

  • Total Structure Weight: 103.19 kDa 
  • Atom Count: 7,632 
  • Modeled Residue Count: 906 
  • Deposited Residue Count: 930 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
A, B, C, D, E
A, B, C, D, E, F
155Dictyostelium discoideumMutation(s): 1 
EC: 2.7.4.6
UniProt
Find proteins for P22887 (Dictyostelium discoideum)
Explore P22887 
Go to UniProtKB:  P22887
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22887
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.32 Å
  • R-Value Free:  0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.201 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.008α = 90
b = 105.79β = 117.23
c = 70.576γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2015-03-25
    Changes: Database references
  • Version 1.2: 2015-04-22
    Changes: Database references
  • Version 1.3: 2020-03-04
    Changes: Derived calculations, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description