9DQC | pdb_00009dqc

Hare calicivirus protruding domain and A-trisaccharide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work: 
    0.155 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of a non-pathogenic hare calicivirus capsid bound to a histo-blood group antigen co-factor.

Hansman, G.S.Reese, T.Pancera, M.Rudd, P.A.Masic, V.Haselhorst, T.von Itzstein, M.

(2024) J Virol 98: e0167524-e0167524


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hare calicivirus protruding domain
A, B
332Hare calicivirus Australia-1Mutation(s): 0 
UniProt
Find proteins for A0A4D6I9J0 (Hare calicivirus Australia-2)
Explore A0A4D6I9J0 
Go to UniProtKB:  A0A4D6I9J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4D6I9J0
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose
C, D
3N/A
Glycosylation Resources
GlyTouCan:  G15611BA
GlyCosmos:  G15611BA
GlyGen:  G15611BA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Work:  0.155 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.11α = 90
b = 82.526β = 90.96
c = 74.331γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-30
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references