4PCG

Structure of Human Polyomavirus 6 (HPyV6) VP1 pentamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure analysis of the major capsid proteins of human polyomaviruses 6 and 7 reveals an obstructed sialic Acid binding site.

Stroh, L.J.Neu, U.Blaum, B.S.Buch, M.H.Garcea, R.L.Stehle, T.

(2014) J.Virol. 88: 10831-10839


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP1
A, B, C, D, E
276Human polyomavirus 6Mutation(s): 0 
Find proteins for D6QWI0 (Human polyomavirus 6)
Go to UniProtKB:  D6QWI0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C, D, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B, C, D, E
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.148 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 183.900α = 90.00
b = 89.440β = 131.26
c = 125.270γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
REFMACrefinement
Cootmodel building
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Baden-Wuerttemberg StiftungGermany--

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Other, Refinement description, Source and taxonomy