SMTL ID : 3mu3.2 (1 other biounit)

Crystal structure of chicken MD-1 complexed with lipid IVa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

LP4.1: 17 residues within 4Å: Chain A: F.30, F.32, A.62, Y.76, E.78, L.80, K.87, L.88, Y.101, P.104, I.105, T.106, A.121, A.132, A.134, F.136 Ligands: LP5.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.30, A:F.32, A:A.62, A:L.88, A:I.105, A:A.132, A:A.134, A:F.136 Hydrogen bonds: A:E.78, A:K.87, A:K.87 Water bridges: A:T.106

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)

LP5.2: 10 residues within 4Å: Chain A: I.19, L.74, Y.76, E.78, L.107, G.108, I.119, F.136, V.138 Ligands: LP4.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.19, A:L.74, A:I.119, A:F.136, A:V.138 Hydrogen bonds: A:Y.76, A:Y.76, A:G.108 Salt bridges: A:K.87

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.100, Y.101, E.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.102, A:E.102, A:E.102 Water bridges: A:E.102 GOL.4: 2 residues within 4Å: Chain A: H.9, T.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.9, A:T.10, A:T.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoon, S.I. et al., Crystal structure of soluble MD-1 and its interaction with lipid IVa. Proc.Natl.Acad.Sci.USA (2010)

Release Date

2010-06-09

Peptides

Protein MD-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Protein MD-1

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