SMTL ID : 5ijc.2 (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

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: 4 residues within 4Å: Chain A: D.61, R.155, V.157, N.173 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain B: S.518, K.519, N.540, S.542, H.543, E.562, W.588 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.519 NAG-NAG.3: 2 residues within 4Å: Chain B: D.65, N.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.65

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

NAG.4: 2 residues within 4Å: Chain A: E.87, N.137 No protein-ligand interaction detected (PLIP) NAG.7: 3 residues within 4Å: Chain B: V.193, N.220, H.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.244 NAG.8: 2 residues within 4Å: Chain B: N.253, S.254 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.253 NAG.9: 2 residues within 4Å: Chain B: N.323, K.345 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.345, B:K.345 NAG.10: 3 residues within 4Å: Chain B: T.485, N.508, T.510 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.485

2 x V2A: neoseptin 3(Non-covalent)

V2A.5: 15 residues within 4Å: Chain A: I.75, L.77, V.105, L.110, F.142, F.144, I.147, F.149, P.150, I.176 Chain B: S.429, F.454, S.455, F.477 Ligands: V2A.6 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.75, A:L.77, A:V.105, A:L.110, A:F.142, A:F.144, A:I.147, A:I.147, A:I.147, A:P.150, A:I.176, B:F.454 Hydrogen bonds: B:S.429, B:S.455, B:S.455 V2A.6: 10 residues within 4Å: Chain A: L.101, I.103, R.113, F.149, Y.154, C.156, F.174 Chain B: R.450, E.453 Ligands: V2A.5 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.101, A:I.103, A:F.149, A:F.174, B:E.453 Hydrogen bonds: A:R.113, A:R.113 pi-Cation interactions: A:R.113

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

Lymphocyte antigen 96

Toll-like receptor 4,Variable lymphocyte receptor B

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