4X16

JC Mad-1 polyomavirus VP1 in complex with GD1a oligosaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

The Greater Affinity of JC Polyomavirus Capsid for alpha 2,6-Linked Lactoseries Tetrasaccharide c than for Other Sialylated Glycans Is a Major Determinant of Infectivity.

Stroh, L.J.Maginnis, M.S.Blaum, B.S.Nelson, C.D.Neu, U.Gee, G.V.O'Hara, B.A.Motamedi, N.DiMaio, D.Atwood, W.J.Stehle, T.

(2015) J.Virol. 89: 6364-6375


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major capsid protein VP1
A, B, C, D, E
272JC polyomavirusMutation(s): 0 
Find proteins for P03089 (JC polyomavirus)
Go to UniProtKB:  P03089
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SIA
Query on SIA

Download SDF File 
Download CCD File 
B, C, D
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.166 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 149.810α = 90.00
b = 95.580β = 110.33
c = 128.790γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
Cootmodel building
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2015-05-27
    Type: Database references
  • Version 2.0: 2018-01-31
    Type: Atomic model, Author supporting evidence, Derived calculations