SMTL ID : 3vq1.1

Crystal structure of mouse TLR4/MD-2/lipid IVa complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.183, H.207, R.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.235, A:R.235 NAG-NAG.2: 7 residues within 4Å: Chain A: S.481, K.482, N.503, S.505, T.525, D.527 Ligands: NAG.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.482 NAG-NAG.3: 8 residues within 4Å: Chain C: S.481, K.482, L.501, N.503, S.505, H.506, D.527 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.482

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

NAG.4: 5 residues within 4Å: Chain A: D.527, S.529, N.551 Ligands: NAG-NAG.2, NAG-NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.527, A:N.551 NAG.7: 7 residues within 4Å: Chain C: D.527, S.529, F.530, N.551, V.578 Ligands: NAG-NAG.3, NAG-NAG.3 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.530 Hydrogen bonds: C:D.527, C:S.529, C:N.551

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

LP4.5: 15 residues within 4Å: Chain A: K.242, Q.318 Chain B: I.36, V.45, V.47, L.58, F.60, L.78, Y.86, I.101, P.102, F.103, S.104, F.135 Ligands: LP5.6 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.36, B:V.45, B:V.47, B:L.58, B:F.60, B:I.101, B:I.101, B:F.103, B:F.135 Hydrogen bonds: B:Y.86, B:S.104, B:S.104, A:K.242 Salt bridges: A:K.242, A:K.242 LP4.8: 14 residues within 4Å: Chain C: K.242, K.339 Chain D: I.36, V.45, V.47, F.60, L.78, Y.86, I.101, P.102, F.103, S.104, F.105 Ligands: LP5.9 15 PLIP interactions: 10 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:V.45, D:V.47, D:F.60, D:L.78, D:I.101, D:F.103, D:F.105 Hydrogen bonds: D:Y.86, D:S.104, D:S.104, C:K.242, C:K.242, C:K.339 Salt bridges: C:K.242, C:K.242

2 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)

LP5.6: 15 residues within 4Å: Chain B: I.36, I.64, L.71, R.74, F.105, E.106, G.107, I.108, F.110, Y.115, C.117 Chain C: S.392, R.413, F.417 Ligands: LP4.5 20 PLIP interactions: 12 interactions with chain B, 6 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:I.36, B:I.64, B:I.64, B:L.71, B:F.105, B:F.105, B:F.110, B:Y.115, C:F.417 Hydrogen bonds: B:R.74, B:E.106, B:G.107, B:I.108, C:S.392, C:S.392, C:S.392, C:R.413, C:R.413 Salt bridges: A:K.339, A:K.339 LP5.9: 15 residues within 4Å: Chain A: S.392, R.413, F.417 Chain D: I.36, I.64, L.71, R.74, F.105, E.106, G.107, I.108, F.110, Y.115, C.117 Ligands: LP4.8 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:I.36, D:I.64, D:L.71, D:F.105, D:F.110, D:F.110, D:Y.115, A:F.417, A:F.417 Hydrogen bonds: D:E.106, D:G.107, A:S.392, A:R.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2. Proc.Natl.Acad.Sci.USA (2012)

Release Date

2012-05-09

Peptides

Toll-like receptor 4: AC
Lymphocyte antigen 96: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

B
C

D
D

Toll-like receptor 4

Lymphocyte antigen 96

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