8EMY

Structure of GII.4 norovirus in complex with Nanobody 82

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Structure of GII.4 norovirus in complex with Nanobody 82

Kher, G., Sabin, C., Pancera, M., Koromyslova, A., Hansman, G.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GII.4 P domain
A, B, C, D, E, F
A, B, C, D, E, F
307NorovirusMutation(s): 0 
UniProt
Find proteins for K4LM89 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU)
Explore K4LM89 
Go to UniProtKB:  K4LM89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK4LM89
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody 82
G, H, I, J, K, L
G, H, I, J, K, L
122Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth D],
EA [auth D],
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth E],
LA [auth E],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
OA [auth E],
P [auth A],
PA [auth F],
Q [auth A],
QA [auth F],
R [auth A],
RA [auth F],
S [auth B],
SA [auth F],
T [auth B],
TA [auth F],
U [auth B],
UA [auth K],
V [auth B],
W [auth B],
X [auth C],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.021α = 90
b = 142.459β = 90
c = 207.969γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release