2E59: Human MD-2

Crystal structure of human MD-2 in complex with lipid IVa. Determined by X-ray diffraction at 2.21 Å resolution. Released 26 Jun 2007.

Method: X-ray diffraction
Resolution: 2.21 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,382
Mol. weight: 18.45 kDa
Ligands: LP4, LP5, NAG
Released: 26 Jun 2007

Explore 2E59 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2E59 contains 5 α-helices and 10 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
β-strand	22-26	5	1
β-strand	30-36	7	1
β-strand	44-49	6	2
α-helix	51-53	3
β-strand	57-65	9	2
β-strand	75-82	8	1
β-strand	85-86	2	1
α-helix	87-89	3
β-strand	90-93	4	1
α-helix	103-106	4
β-strand	113-121	9	2
β-strand	130-139	10	1
β-strand	144-155	12	1
α-helix	156	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lymphocyte antigen 96	A	protein	144	Homo sapiens	Q9Y6Y9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2E59_1 Lymphocyte antigen 96 (chains A)
EAQKQYWVCNSSDASISYTYCDKMQYPISINVNPCIELKGSKGLLHIFYIPRRDLKQLYF
NLYITVNTMNLPKRKEVICRGSDDDYSFCRALKGETVNTTISFSFKGIKFSKGKYKCVVE
AISGSPEEMLFCLEFVILHQPNSN

Ligands and cofactors

ID	Name	Formula	Copies
LP4	2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino…	C34 H66 N O12 P	1
LP5	(r)-((2R,3S,4R,5R,6R)-3-hydroxy-2-(hydroxymethyl)-5-((R)-3-hydroxytetradecanami…	C34 H66 N O12 P	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa. Ohto, U., Fukase, K., Miyake, K. et al. Science (2007) 316:1632-1634. DOI 10.1126/science.1139111 · PubMed

Other PDB entries of the same protein (UniProt Q9Y6Y9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2E56 2.0 Å, Crystal structure of human MD-2
8WO1 2.24 Å, Cryo-EM Structure of Human TLR4/MD-2/DLAM5 Complex
4G8A 2.4 Å, Crystal structure of human TLR4 polymorphic variant D299G and T399I in complex with MD-2…
2Z65 2.7 Å, Crystal structure of the human TLR4 TV3 hybrid-MD-2-Eritoran complex
9J03 2.7 Å, Cyro-EM Structure of Human TLR4/MD-2/DLAM1 Complex
8WTA 2.9 Å, Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex
3FXI 3.1 Å, Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex
3ULA 3.6 Å, Crystal structure of the TV3 mutant F63W-MD-2-Eritoran complex

Browse structure collections

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