4DW5

Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with a non-cleavable CpU dinucleotide

Structural Biology Knowledgebase: 4DW5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.216

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4DW5

Classification: VIRAL PROTEIN

Total Structure Weight: 45285.53

Macromolecule Entities
Molecule Chains Length Organism Details
E(rns) glycoprotein A, B 167 Bovine viral diarrhea virus 1 Fragment: N-terminal fragment
Gene Name(s):

Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CSQ
Query on CSQ

A O-[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin- 1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran- 3-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4- dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran- 2-yl]methyl} hydrogen (R)-phosphorothioate
C18 H24 N5 O12 P S
VZQLNJPTHATNOF-ILIYZMILSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CSV
Query on CSV

A O-[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin- 1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran- 3-yl] O-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4- dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran- 2-yl]methyl} hydrogen (S)-phosphorothioate
C18 H24 N5 O12 P S
VZQLNJPTHATNOF-OXIRAOGTSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
U
Query on U

B URIDINE-5'-MONOPHOSPHATE
C9 H13 N2 O9 P
DJJCXFVJDGTHFX-XVFCMESISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1PE
Query on 1PE

A PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A, B BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.216
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 105.34 α = 90.00
b = 105.34 β = 90.00
c = 211.26 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-24
  • Released Date: 2012-05-23
  • Deposition author(s): Krey, T., Bontems, F., Vonrhein, C., Vaney, M.-C., Bricogne, G., Ruemenapf, T., Rey, F.A.

Revision History

No revisions since initial release