SMTL ID : 8wsa.1

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM5 Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.132 No protein-ligand interaction detected (PLIP) NAG.2: 2 residues within 4Å: Chain A: E.46, N.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.46 NAG.7: 4 residues within 4Å: Chain B: K.478, N.499, D.523 Ligands: NAG.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.478, B:K.478, B:D.523, B:D.523 NAG.8: 3 residues within 4Å: Chain B: C.255, H.278, N.282 No protein-ligand interaction detected (PLIP) NAG.9: 2 residues within 4Å: Chain B: V.152, N.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.179 NAG.10: 1 residues within 4Å: Chain B: N.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.212 NAG.11: 3 residues within 4Å: Chain B: F.526, N.547 Ligands: NAG.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.547 NAG.14: 1 residues within 4Å: Chain C: N.132 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain C: E.46, N.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.46 NAG.19: 4 residues within 4Å: Chain D: K.478, N.499, D.523 Ligands: NAG.23 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.478, D:K.478, D:D.523, D:D.523 NAG.20: 3 residues within 4Å: Chain D: C.255, H.278, N.282 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain D: V.152, N.179 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.179 NAG.22: 1 residues within 4Å: Chain D: N.212 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.212 NAG.23: 3 residues within 4Å: Chain D: F.526, N.547 Ligands: NAG.19 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.547

2 x 2IL: (3R)-3-(dodecanoyloxy)tetradecanoic acid(Non-covalent)

2IL.3: 5 residues within 4Å: Chain A: I.135 Ligands: 0IL.4, X6N.5, 01.6, GP4.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.135 2IL.16: 5 residues within 4Å: Chain C: I.135 Ligands: 01.13, 0IL.17, X6N.18, GP4.24 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.135

2 x 0IL: (3R)-3-(tetradecanoyloxy)tetradecanoic acid(Covalent)

0IL.4: 6 residues within 4Å: Chain A: V.45, F.47, Y.84, F.133 Ligands: 2IL.3, GP4.12 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.45, A:V.45, A:F.47, A:F.133 Salt bridges: B:K.335 0IL.17: 7 residues within 4Å: Chain C: V.45, F.47, F.58, Y.84, F.133 Ligands: 2IL.16, GP4.24 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:V.45, C:V.45, C:F.47, C:F.58, C:F.133 Salt bridges: D:K.335

2 x X6N: [(2~{R},3~{S},4~{R},5~{S})-2-(hydroxymethyl)-5-methoxy-4,6-bis(oxidanyl)oxan-3-yl] dihydrogen phosphate(Non-covalent)

X6N.5: 4 residues within 4Å: Chain A: E.104 Ligands: 2IL.3, 01.6, GP4.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.104 X6N.18: 5 residues within 4Å: Chain C: E.104 Chain D: Q.314 Ligands: 01.13, 2IL.16, GP4.24 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.314, C:E.104

2 x 01: (3~{S})-3-decanoyloxytetradecanoic acid

01.6: 9 residues within 4Å: Chain A: I.34, R.72, E.104, I.106, F.108, Y.113 Chain D: S.388 Ligands: 2IL.3, X6N.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.34, A:I.106, A:F.108, A:Y.113 01.13: 10 residues within 4Å: Chain B: S.388 Chain C: I.34, R.72, F.103, E.104, I.106, F.108, Y.113 Ligands: 2IL.16, X6N.18 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.103, C:I.106, C:F.108, C:Y.113

2 x GP4: 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose(Post Translational Modification)(Non-covalent)

GP4.12: 4 residues within 4Å: Chain B: K.335 Ligands: 2IL.3, 0IL.4, X6N.5 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.335 GP4.24: 4 residues within 4Å: Chain D: K.335 Ligands: 2IL.16, 0IL.17, X6N.18 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:K.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, Y. et al., Structural insight on tailored modulation of TLR4-mediated pro-inflammatory response by disaccharide lipid A mimetics. To Be Published

Release Date

2024-10-23

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
D

B
A

D
B

Lymphocyte antigen 96

Toll-like receptor 4

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