SMTL ID : 5ijc.1 (1 other biounit)

The crystal structure of mouse TLR4/MD-2/neoseptin-3 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-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: 4 residues within 4Å: Chain A: V.193, N.220, H.244, R.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272, A:R.272 NAG-NAG.2: 7 residues within 4Å: Chain A: S.518, K.519, N.540, S.542, H.543, E.562, W.588 No protein-ligand interaction detected (PLIP)

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

NAG.3: 2 residues within 4Å: Chain A: N.253, R.282 No protein-ligand interaction detected (PLIP) NAG.4: 3 residues within 4Å: Chain A: H.319, N.323, K.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.345 NAG.5: 1 residues within 4Å: Chain A: N.508 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain A: Y.185, S.187, N.188 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.184 NAG.9: 2 residues within 4Å: Chain B: E.87, N.137 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.87, B:N.137 NAG.10: 4 residues within 4Å: Chain B: C.60, D.61, R.155, N.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.61, B:N.173

2 x V2A: neoseptin 3(Non-covalent)

V2A.7: 15 residues within 4Å: Chain A: S.429, F.454, S.455, F.477 Chain B: I.75, L.77, V.105, L.110, F.142, F.144, I.147, F.149, P.150, I.176 Ligands: V2A.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:I.75, B:I.75, B:L.77, B:V.105, B:L.110, B:F.142, B:F.144, B:F.144, B:I.147, B:F.149, B:F.149, B:P.150, B:I.176, A:F.454 Hydrogen bonds: A:S.429, A:S.455, A:S.455 V2A.8: 12 residues within 4Å: Chain A: R.450, E.453 Chain B: L.101, I.103, R.113, E.115, F.149, Y.154, C.156, F.174, I.176 Ligands: V2A.7 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.101, B:I.103, B:F.149, B:F.174, B:I.176, A:E.453 Hydrogen bonds: B:E.115

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Toll-like receptor 4,Variable lymphocyte receptor B

Lymphocyte antigen 96

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