SMTL ID : 5ijd.3 (2 other biounits)

The crystal structure of mouse TLR4/MD-2/lipid A complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

4 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: 4 residues within 4Å: Chain A: D.20, H.21, R.114, N.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.114 NAG-NAG.2: 4 residues within 4Å: Chain B: V.152, N.179, H.203, R.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.231, B:R.231 NAG-NAG.3: 2 residues within 4Å: Chain B: H.278, N.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.282 NAG-NAG.4: 6 residues within 4Å: Chain B: S.477, K.478, N.499, S.501, H.502, W.547 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.478, B:K.478

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

NAG.5: 2 residues within 4Å: Chain A: E.46, N.96 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain B: N.467 No protein-ligand interaction detected (PLIP)

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

LP4.6: 13 residues within 4Å: Chain A: I.34, V.43, L.56, L.76, Y.84, I.99, P.100, F.101, S.102 Chain B: K.238 Ligands: LP5.7, DAO.8, MYR.9 8 PLIP interactions: 1 interactions with chain B, 7 interactions with chain A Salt bridges: B:K.238 Hydrophobic interactions: A:I.34, A:V.43, A:L.56, A:L.76, A:I.99 Hydrogen bonds: A:S.102, A:S.102

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)

LP5.7: 12 residues within 4Å: Chain A: L.69, R.72, F.103, E.104, G.105, I.106, F.108, P.109, F.133 Ligands: LP4.6, DAO.8, MYR.9 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.69, A:F.103, A:F.103, A:I.106, A:F.108, A:F.108, A:F.133, A:F.133 Hydrogen bonds: A:E.104, A:E.104, A:E.104, A:I.106

1 x DAO: LAURIC ACID(Non-covalent)

DAO.8: 8 residues within 4Å: Chain A: L.60, I.62, R.72, E.74, Y.113 Ligands: LP4.6, LP5.7, MYR.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.60, A:I.62, A:Y.113

1 x MYR: MYRISTIC ACID(Non-covalent)

MYR.9: 8 residues within 4Å: Chain A: F.58, E.74, A.117, L.131, F.133 Ligands: LP4.6, LP5.7, DAO.8 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.58, A:F.58, A:E.74, A:A.117, A:L.131, A:F.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Y. et al., TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-04-27

Peptides

Lymphocyte antigen 96: A
Toll-like receptor 4, Variable lymphocyte receptor B chimera: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
B

Lymphocyte antigen 96

Toll-like receptor 4, Variable lymphocyte receptor B chimera

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