SMTL ID : 3vq2.1

Crystal structure of mouse TLR4/MD-2/LPS complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

hetero-2-2-mer

Ligands

2 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: 8 residues within 4Å: Chain A: S.481, K.482, L.501, N.503, S.505, H.506, D.527 Ligands: NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.482 NAG-NAG.2: 6 residues within 4Å: Chain C: S.481, K.482, N.503, S.505, T.525, D.527 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.482

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

NAG.3: 6 residues within 4Å: Chain A: G.125, Q.126, A.147, Y.148, S.150, N.151 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.151 NAG.4: 3 residues within 4Å: Chain A: N.183, S.185, H.207 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.185 NAG.5: 5 residues within 4Å: Chain A: D.527, S.529, N.551 Ligands: NAG-NAG.1, NAG-NAG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.527, A: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)

LP4.6: 18 residues within 4Å: Chain A: K.242 Chain B: I.36, V.45, F.49, L.55, L.58, F.60, L.78, Y.86, F.88, I.101, P.102, F.103, S.104, F.105 Ligands: LP5.7, DAO.8, MYR.9 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.36, B:V.45, B:F.49, B:L.55, B:L.58, B:F.60, B:L.78, B:F.88, B:I.101, B:F.103, B:F.105 Hydrogen bonds: B:P.102, B:S.104, B:S.104 Salt bridges: A:K.242 LP4.10: 19 residues within 4Å: Chain C: K.242 Chain D: I.36, V.45, V.47, F.49, L.55, L.58, F.60, L.78, Y.86, F.88, I.101, P.102, F.103, S.104, F.105 Ligands: LP5.11, DAO.12, MYR.13 15 PLIP interactions: 14 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:V.45, D:V.47, D:F.49, D:L.55, D:L.58, D:F.60, D:L.78, D:F.88, D:I.101, D:F.103, D:F.105 Hydrogen bonds: D:P.102, D:S.104, D:S.104 Salt bridges: 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)

LP5.7: 17 residues within 4Å: Chain A: K.339 Chain B: L.38, V.66, L.71, R.74, F.105, E.106, G.107, I.108, F.110, F.135 Chain C: S.392, R.413, F.417 Ligands: LP4.6, DAO.8, MYR.9 21 PLIP interactions: 15 interactions with chain B, 4 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:L.38, B:V.66, B:L.71, B:F.105, B:F.105, B:F.105, B:I.108, B:F.110, B:F.110, B:F.110, B:F.135, C:F.417 Hydrogen bonds: B:R.74, B:E.106, B:G.107, B:I.108, C:S.392, C:S.392, C:R.413 Salt bridges: A:K.339, A:K.339 LP5.11: 17 residues within 4Å: Chain A: S.392, E.416, F.417 Chain D: L.38, V.66, L.71, R.74, F.105, E.106, G.107, I.108, F.110, F.135, I.137 Ligands: LP4.10, DAO.12, MYR.13 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:V.66, D:L.71, D:F.105, D:F.105, D:I.108, D:F.110, D:F.110, D:F.135, D:F.135, D:I.137, A:F.417, A:F.417 Hydrogen bonds: D:E.106, D:G.107, D:I.108, A:S.392, A:S.392

2 x DAO: LAURIC ACID(Non-covalent)

DAO.8: 8 residues within 4Å: Chain B: L.62, I.64, R.74, E.76, F.110, Y.115 Ligands: LP4.6, LP5.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.62, B:I.64, B:F.110, B:Y.115 DAO.12: 6 residues within 4Å: Chain D: L.38, R.74, F.110, Y.115 Ligands: LP4.10, LP5.11 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.38, D:F.110, D:Y.115

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.9: 8 residues within 4Å: Chain B: I.30, F.60, E.76, A.119, F.131, L.133 Ligands: LP4.6, LP5.7 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.30, B:E.76, B:A.119, B:F.131, B:L.133 MYR.13: 10 residues within 4Å: Chain D: I.30, F.60, L.62, E.76, V.77, A.119, F.131, L.133 Ligands: LP4.10, LP5.11 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.30, D:F.60, D:F.60, D:L.62, D:E.76, D:A.119, D:F.131, D:L.133

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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