6H6M

CR10 murine norovirus protruding domain in complex with the CD300lf receptor and glycochenodeoxycholate (GCDCA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal structures of murine norovirus protruding domain with conjugated bile acid reveal a novel binding pocket.

Kilic, T.Koromyslova, A.Malak, V.Hansman, G.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid proteinA, B, C, D303Murine norovirus GV/CR10/2005/USAMutation(s): 0 
UniProt
Find proteins for A7YK37 (Murine norovirus GV/CR10/2005/USA)
Explore A7YK37 
Go to UniProtKB:  A7YK37
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7YK37
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CMRF35-like molecule 1E, F111Mus musculusMutation(s): 0 
Gene Names: Cd300lfClm1Lmir3
UniProt
Find proteins for Q6SJQ7 (Mus musculus)
Explore Q6SJQ7 
Go to UniProtKB:  Q6SJQ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6SJQ7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CHO
Query on CHO

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B],
S [auth C],
X [auth D]
GLYCOCHENODEOXYCHOLIC ACID
C26 H43 N O5
GHCZAUBVMUEKKP-GYPHWSFCSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
EA [auth F]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CA [auth E]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth E],
DA [auth F],
H [auth A],
I [auth A],
AA [auth D],
BA [auth E],
DA [auth F],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B],
W [auth C],
Y [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.94α = 90
b = 137.55β = 95.84
c = 93.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release