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: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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


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
EC: 3.2.2.6
Find proteins for O00206 (Homo sapiens)
Go to UniProtKB:  O00206
NIH Common Fund Data Resources
PHAROS  O00206

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lymphocyte antigen 96
C, D
144Homo sapiensMutation(s): 1 
Gene Names: LY96ESOP1MD2
Find proteins for Q9Y6Y9 (Homo sapiens)
Go to UniProtKB:  Q9Y6Y9
NIH Common Fund Data Resources
PHAROS  Q9Y6Y9
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LP4
Query on LP4

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
LP5
Query on LP5

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 CCD File 
C, D
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
MYR
Query on MYR

Download CCD File 
C, D
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
DAO
Query on DAO

Download CCD File 
C, D
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.038α = 90
b = 124.68β = 115.72
c = 109.14γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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
    Changes: Database references, Non-polymer description