2E59

Crystal structure of human MD-2 in complex with lipid IVa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa

Ohto, U., Fukase, K., Miyake, K., Satow, Y.

(2007) Science 316: 1632-1634

  • DOI: 10.1126/science.1139111
  • Primary Citation of Related Structures:  
    2E59, 2E56

  • PubMed Abstract: 

    • Endotoxic lipopolysaccharide (LPS) with potent immunostimulatory activity is recognized by the receptor complex of MD-2 and Toll-like receptor 4. Crystal structures of human MD-2 and its complex with the antiendotoxic tetra-acylated lipid A core of LPS h ...

    Endotoxic lipopolysaccharide (LPS) with potent immunostimulatory activity is recognized by the receptor complex of MD-2 and Toll-like receptor 4. Crystal structures of human MD-2 and its complex with the antiendotoxic tetra-acylated lipid A core of LPS have been determined at 2.0 and 2.2 angstrom resolutions, respectively. MD-2 shows a deep hydrophobic cavity sandwiched by two beta sheets, in which four acyl chains of the ligand are fully confined. The phosphorylated glucosamine moieties are located at the entrance to the cavity. These structures suggest that MD-2 plays a principal role in endotoxin recognition and provide a basis for antiseptic drug development.

    Organizational Affiliation: 

    Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lymphocyte antigen 96 A144Homo sapiensMutation(s): 0 
Gene Names: LY96, ESOP1, MD2
Find proteins for Q9Y6Y9 (Homo sapiens)
Explore Q9Y6Y9 
Go to UniProtKB:  Q9Y6Y9
NIH Common Fund Data Resources
PHAROS:  Q9Y6Y9
GTEx:  ENSG00000154589
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LP5
Query on LP5
Download Ideal Coordinates CCD File 
A
(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
LP4
Query on LP4
Download Ideal Coordinates CCD File 
A
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
NAG
Query on NAG
Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.795α = 90
b = 52.795β = 90
c = 110.889γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-12-19 
  • Released Date: 2007-06-26 
    • Deposition Author(s): Ohto, U., Satow, Y.

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary