4G8A

Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2 and LPS

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structural analyses of human Toll-like receptor 4 polymorphisms D299G and T399I

Ohto, U., Yamakawa, N., Akashi-Takamura, S., Miyake, K., Shimizu, T.

(2012) J.Biol.Chem. 287: 40611-40617

  • DOI: 10.1074/jbc.M112.404608

  • PubMed Abstract: 

    • TLR4 polymorphism replacing Asp-299 with Gly and Thr-399 with Ile (D299G/T399I) causes LPS hyporesponsiveness.

    TLR4 polymorphism replacing Asp-299 with Gly and Thr-399 with Ile (D299G/T399I) causes LPS hyporesponsiveness.

    Organizational Affiliation: 

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Toll-like receptor 4
A, B
635Homo sapiensMutation(s): 2 
Gene Names: TLR4
Find proteins for O00206 (Homo sapiens)
Go to Gene View: TLR4
Go to UniProtKB:  O00206
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lymphocyte antigen 96
C, D
144Homo sapiensMutation(s): 1 
Gene Names: LY96 (ESOP1, MD2)
Find proteins for Q9Y6Y9 (Homo sapiens)
Go to Gene View: LY96
Go to UniProtKB:  Q9Y6Y9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR
Download SDF File 
Download CCD File 
C, D
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
LP5
Query on LP5
Download SDF File 
Download CCD File 
C, D
(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
C34 H66 N O12 P
HEHQDWUWJVPREQ-XQJZMFRCSA-N
 Ligand Interaction
KDO
Query on KDO
Download SDF File 
Download CCD File 
C, D
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
DAO
Query on DAO
Download SDF File 
Download CCD File 
C, D
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
LP4
Query on LP4
Download SDF File 
Download CCD File 
C, D
2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose
C34 H66 N O12 P
AJRPJFBMHCTNGK-XQJZMFRCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 158.038α = 90.00
b = 124.680β = 115.72
c = 109.140γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2012-07-23 
  • Released Date: 2012-10-17 
  • Deposition Author(s): Ohto, U., Shimizu, T.

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references, Non-polymer description