4MJ0

BK Polyomavirus VP1 pentamer in complex with GD3 oligosaccharide

Structural Biology Knowledgebase: 4MJ0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.177
  • R-Value Work: 0.150

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4MJ0

Classification: viral protein

Total Structure Weight: 155016.47

Macromolecule Entities
Molecule Chains Length Organism Details
VP1 capsid protein A, B, C, D, E 275 Bk polyomavirus Gene Name(s):

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SIA
Query on SIA

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

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

A BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D, E CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.177
  • R-Value Work: 0.150
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 144.68 α = 90.00
b = 152.64 β = 90.00
c = 63.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-09-03
  • Released Date: 2013-11-06
  • Deposition author(s): Neu, U., Stroh, L.J., Stehle, T.

Revision History

No revisions since initial release