6BXC

Crystal structure of N-terminal fragment of Zebrafish Toll-Like Receptor 5 (TLR5) with Lamprey Variable Lymphocyte Receptor 9 (VLR9) bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

VLR Recognition of TLR5 Expands the Molecular Characterization of Protein Antigen Binding by Non-Ig-based Antibodies.

Gunn, R.J.Herrin, B.R.Acharya, S.Cooper, M.D.Wilson, I.A.

(2018) J. Mol. Biol. 430: 1350-1367


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 5b, Variable lymphocyte receptor B chimera
A, B
455Eptatretus burgeriDanio rerio
This entity is chimeric
Mutation(s): 0 
Gene Names: VLRB, tlr5b
Find proteins for Q4G1L2 (Eptatretus burgeri)
Go to UniProtKB:  Q4G1L2
Find proteins for F8W3J5 (Danio rerio)
Go to UniProtKB:  F8W3J5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Variable Lymphocyte Receptor 9 (VLR9)
D, C
178N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
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: 0.270 
  • R-Value Work: 0.230 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.380α = 112.14
b = 69.413β = 104.12
c = 84.561γ = 100.81
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesA1042266
National Institutes of HealthUnited StatesAI072435

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release