RCSB PDB - 2E56: Crystal structure of human MD-2 (original) (raw)
Crystal structure of human MD-2
This is version 1.4 of the entry. See complete history.
Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa.
[Ohto, U.](/search?q=citation.rcsb%5Fauthors:Ohto, U.), [Fukase, K.](/search?q=citation.rcsb%5Fauthors:Fukase, K.), [Miyake, K.](/search?q=citation.rcsb%5Fauthors:Miyake, K.), [Satow, Y.](/search?q=citation.rcsb%5Fauthors:Satow, Y.)
(2007) Science 316: 1632-1634
PubMed: 17569869 Search on PubMed
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 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.
Macromolecule Content
- Total Structure Weight: 17.71 kDa
- Atom Count: 1,397
- Modelled Residue Count: 144
- Deposited Residue Count: 144
- Unique protein chains: 1
Find similar proteins by:
(by identity cutoff) | 3D Structure
Experimental Data & Validation
Experimental Data
- Space Group: [P 41 21 2](/search?q=symmetry.space%5Fgroup%5Fname%5FH%5FM:P 41 21 2)
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.113 | α = 90 |
| b = 53.113 | β = 90 |
| c = 111.447 | γ = 90 |
Software Package:
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHARP | phasing |
Revision History (Full details and data files)
- 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 - Version 1.4: 2024-11-06
Changes: Data collection, Database references, Structure summary