SMTL ID : 2e59.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

monomer

Ligands

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.10, S.15, Q.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.10, A:S.15, A:Q.140 NAG.2: 3 residues within 4Å: Chain A: H.46, F.48, N.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.100

1 x LP5: (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE(Non-covalent)

LP5.3: 16 residues within 4Å: Chain A: I.30, L.45, I.47, Y.49, L.58, F.60, L.62, E.76, Y.86, F.88, I.101, S.102, F.103, S.104, K.106 Ligands: LP4.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:I.30, A:L.45, A:I.47, A:Y.49, A:L.58, A:F.60, A:F.60, A:F.60, A:L.62, A:F.88, A:F.88, A:I.101 Hydrogen bonds: A:S.104 Water bridges: A:K.106, A:K.106, A:K.106

1 x LP4: 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose(Non-covalent)

LP4.4: 11 residues within 4Å: Chain A: I.36, I.64, R.74, S.104, F.105, K.106, I.108, C.117, F.135, I.137 Ligands: LP5.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.36, A:I.64, A:F.105, A:F.135, A:I.137 Hydrogen bonds: A:K.106 Water bridges: A:R.74, A:R.74, A:R.74, A:G.107, A:G.107 Salt bridges: A:R.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa. Science (2007)

Release Date

2007-06-26

Peptides

Lymphocyte antigen 96: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lymphocyte antigen 96

Related Entries With Identical Sequence