1ND2

The structure of Rhinovirus 16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds

Zhang, Y.Simpson, A.A.Ledford, R.M.Bator, C.M.Chakravarty, S.Skochko, G.A.Demenczuk, T.M.Watanyar, A.Pevear, D.C.Rossmann, M.G.

(2004) J.Virol. 78: 11061-11069

  • DOI: 10.1128/JVI.78.20.11061-11069.2004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of huma ...

    Pleconaril is a broad-spectrum antirhinovirus and antienterovirus compound that binds into a hydrophobic pocket within viral protein 1, stabilizing the capsid and resulting in the inhibition of cell attachment and RNA uncoating. When crystals of human rhinovirus 16 (HRV16) and HRV14 are incubated with pleconaril, drug occupancy in the binding pocket is lower than when pleconaril is introduced during assembly prior to crystallization. This effect is far more marked in HRV16 than in HRV14 and is more marked with pleconaril than with other compounds. These observations are consistent with virus yield inhibition studies and radiolabeled drug binding studies showing that the antiviral effect of pleconaril against HRV16 is greater on the infectivity of progeny virions than the parent input viruses. These data suggest that drug integration into the binding pocket during assembly, or at some other late stage in virus replication, may contribute to the antiviral activity of capsid binding compounds.


    Organizational Affiliation

    Department of Biological Sciences, Lilly Hall, Purdue University, 915 W. State St., West Lafayette, IN 47907-2054, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
coat protein VP1
A
285Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
coat protein VP2
B
261Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
coat protein VP3
C
238Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
coat protein VP4
D
68Human rhinovirus 16Mutation(s): 0 
Find proteins for Q82122 (Human rhinovirus 16)
Go to UniProtKB:  Q82122
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
A, D
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.202 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 360.374α = 90.00
b = 343.626β = 90.00
c = 332.650γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance