5AWA

Crystal structure of human TLR8 in complex with MB-568


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based Design of Human TLR8-specific Agonists with Augmented Potency and Adjuvanticity

Beesu, M.Caruso, G.Salyer, A.C.D.Khetani, K.K.Sil, D.Weerasinghe, M.Tanji, H.Ohto, U.Shimizu, T.David, S.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 8
A
811Homo sapiensMutation(s): 0 
Gene Names: TLR8
Find proteins for Q9NR97 (Homo sapiens)
Go to Gene View: TLR8
Go to UniProtKB:  Q9NR97
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M8D
Query on M8D

Download SDF File 
Download CCD File 
A
5-[[3-(aminomethyl)phenyl]methyl]-3-pentyl-quinolin-2-amine
C22 H27 N3
MJTYFAQITQYOAV-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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: 2.2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 139.057α = 90.00
b = 102.379β = 106.82
c = 72.077γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Data collection, Derived calculations