5Y3M

Crystal structure of bovine TLR9 in complex with two DNAs (CpG DNA and TCGTTT DNA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation

Ohto, U.Ishida, H.Shibata, T.Sato, R.Miyake, K.Shimizu, T.

(2018) Immunity 48: 649-658.e4


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 9
A, B
801Bos taurusMutation(s): 0 
Gene Names: TLR9
Find proteins for Q5I2M5 (Bos taurus)
Go to Gene View: TLR9
Go to UniProtKB:  Q5I2M5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*GP*T)-3')E,F6synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*GP*CP*GP*TP*T)-3')D,C10synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.225 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.177α = 90.00
b = 68.693β = 100.64
c = 153.535γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-07-29 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Ohto, U., Shimizu, T.

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-05-02
    Type: Data collection, Database references