› 2e59

X-ray diffraction
2.21Å resolution

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

Released:
DOI: 10.2210/pdb2e59/pdb
PDB entry 2e59 coloured by chain, front view.
PDB entry 2e59 coloured by chain, side view.
PDB entry 2e59 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa.
Ohto U, Fukase K, Miyake K, Satow Y
Science 316 1632-4 (2007)
PMID: 17569869

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195400 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lymphocyte antigen 96 Chain: A
Molecule details ›
Chain: A
Length: 144 amino acids
Theoretical weight: 16.59 KDa
Source organism: Homo sapiens
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q9Y6Y9 (Residues: 17-160; Coverage: 100%)
Gene names: ESOP1, LY96, MD2
Sequence domains: ML domain
Structure domains: Immunoglobulin-like

Ligands and Environments

3 bound ligands:
Ligand NAG 2 x NAG
Ligand LP5 1 x LP5
Ligand LP4 1 x LP4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P41212
Unit cell:
a: 52.795Å b: 52.795Å c: 110.889Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.263
Expression system: Komagataella pastoris

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Citations

80 review citations

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55 mentions without citation

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