2E59

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

• PDB DOI: https://doi.org/10.2210/pdb2E59/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


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

---

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 

Starting Model: experimental

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

• PubMed: 17569869 
• DOI: https://doi.org/10.1126/science.1139111
• Primary Citation of Related Structures:  
  2E56, 2E59


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18.45 kDa 
• Atom Count: 1,382 
• Modelled Residue Count: 144 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	A	144	Homo sapiens	Mutation(s): 0  Gene Names: LY96, ESOP1, MD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Y9 (Homo sapiens) Explore Q9Y6Y9  Go to UniProtKB:  Q9Y6Y9
PHAROS:  Q9Y6Y9 GTEx:  ENSG00000154589
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q9Y6Y9-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LP4	E [auth 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
LP5	D [auth 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
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 52.795	α = 90
b = 52.795	β = 90
c = 110.889	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• 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
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-23
  Changes: Structure summary