5CPW

Crystal structure of murine polyomavirus PTA strain VP1 in complex with the GT1a glycan


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 5CPW

Classification: VIRAL PROTEIN

Total Structure Weight: 165509.20

Macromolecule Entities
Molecule Chains Length Organism Details
VP1 A, B, C, D, E 284 Mus musculus polyomavirus 1 Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SIA
Query on SIA

A, B, C, D, E O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NGA
Query on NGA

A, B, C, D, E N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GAL
Query on GAL

A, B, C, D, E BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D, E GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.160
  • Space Group: P 31 2 1

Unit Cell:

Length (Å) Angle (°)
a = 219.60 α = 90.00
b = 219.60 β = 90.00
c = 99.74 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-07-21
  • Released Date: 2015-10-28
  • Deposition author(s): Liaci, A.M., Buch, M.H.C., Neu, U., Stehle, T.

Revision History

  • Version 1_0: 2015-10-28

    Type: Initial release

  • Version 1_1: 2017-09-06

    Type: Author supporting evidence