SMTL ID : 3m7o.1 (3 other biounits)

Crystal structure of mouse MD-1 in complex with phosphatidylcholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

NAG.1: 7 residues within 4Å: Chain A: K.29, V.41, Y.42, Q.43, N.156, A.157, T.158 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.41 Hydrogen bonds: A:Q.43, A:N.156 NAG.2: 3 residues within 4Å: Chain A: S.93, I.94, N.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.93, A:S.93, A:N.96

1 x L9R: (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

L9R.3: 21 residues within 4Å: Chain A: V.40, I.55, I.62, I.85, L.87, Y.97, L.101, Y.122, P.125, V.126, N.127, P.129, L.131, V.133, P.134, Y.138, L.142, L.144, A.153, C.154, A.155 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:V.40, A:I.55, A:L.87, A:L.101, A:L.101, A:Y.122, A:V.126, A:V.126, A:L.131, A:V.133, A:P.134, A:Y.138, A:L.142, A:L.144, A:A.153 Hydrogen bonds: A:Y.97

5 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.4: 7 residues within 4Å: Chain A: D.84, I.85, T.86, N.96, Y.97, S.98 Ligands: BEN.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.84, A:N.96 Hydrogen bonds: A:D.84, A:S.98 BEN.5: 5 residues within 4Å: Chain A: D.84, E.143, Y.145 Ligands: BEN.4, BEN.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.84, A:E.143 BEN.6: 5 residues within 4Å: Chain A: E.143, Y.145, R.149, T.151 Ligands: BEN.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.145, A:Y.145 Hydrogen bonds: A:E.143 BEN.7: 5 residues within 4Å: Chain A: F.82, Y.145, N.146, E.147, R.149 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.82, A:Y.145, A:R.149 Hydrogen bonds: A:E.147 BEN.8: 7 residues within 4Å: Chain A: G.52, L.53, S.54, R.69, F.70, G.71, Y.121 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.69, A:Y.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harada, H. et al., Crystal structure of mouse MD-1 with endogenous phospholipid bound in its cavity. J.Mol.Biol. (2010)

Release Date

2010-06-09

Peptides

Lymphocyte antigen 86: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lymphocyte antigen 86

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