5VX9

VP8* of P[6] Human Rotavirus RV3 in complex with LNFP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Glycan recognition in globally dominant human rotaviruses.

Hu, L.Sankaran, B.Laucirica, D.R.Patil, K.Salmen, W.Ferreon, A.C.M.Tsoi, P.S.Lasanajak, Y.Smith, D.F.Ramani, S.Atmar, R.L.Estes, M.K.Ferreon, J.C.Prasad, B.V.V.

(2018) Nat Commun 9: 2631-2631


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Outer capsid protein VP4
A
161Human rotavirus AMutation(s): 0 
Find proteins for D7F7M7 (Human rotavirus A)
Go to UniProtKB:  D7F7M7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.510α = 90.00
b = 42.630β = 90.00
c = 95.070γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
iMOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI36040
The Robert Welch foundationUnited StatesQ1279

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release