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

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

GP4.1: 5 residues within 4Å: Chain A: R.312, K.335 Ligands: 2IL.14, 0IL.15, X6N.16 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.312, A:K.335 GP4.8: 4 residues within 4Å: Chain B: K.335 Ligands: 2IL.20, 0IL.21, X6N.22 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.335

2 x 01: (3~{S})-3-decanoyloxytetradecanoic acid(Post Translational Modification)(Covalent)

01.2: 9 residues within 4Å: Chain A: S.388 Chain D: I.34, R.72, E.104, I.106, F.108, Y.113 Ligands: 2IL.20, X6N.22 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.34, D:I.106, D:F.108, D:Y.113 01.17: 9 residues within 4Å: Chain B: S.388 Chain C: I.34, R.72, E.104, I.106, F.108, Y.113 Ligands: 2IL.14, X6N.16 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.34, C:I.106, C:F.108, C:Y.113

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

NAG.3: 4 residues within 4Å: Chain A: K.478, N.499, D.523 Ligands: NAG.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.478, A:K.478, A:D.523, A:D.523 NAG.4: 3 residues within 4Å: Chain A: C.255, H.278, N.282 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: V.152, N.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.179 NAG.6: 1 residues within 4Å: Chain A: N.212 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.212 NAG.7: 3 residues within 4Å: Chain A: F.526, N.547 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.547 NAG.9: 4 residues within 4Å: Chain B: K.478, N.499, D.523 Ligands: NAG.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.478, B:K.478, B:D.523, B:D.523 NAG.10: 3 residues within 4Å: Chain B: C.255, H.278, N.282 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: V.152, N.179 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.179 NAG.12: 1 residues within 4Å: Chain B: N.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.212 NAG.13: 3 residues within 4Å: Chain B: F.526, N.547 Ligands: NAG.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.547 NAG.18: 1 residues within 4Å: Chain C: N.132 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain C: E.46, N.96 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.46 NAG.23: 1 residues within 4Å: Chain D: N.132 No protein-ligand interaction detected (PLIP) NAG.24: 2 residues within 4Å: Chain D: E.46, N.96 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.46

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

2IL.14: 5 residues within 4Å: Chain C: I.135 Ligands: GP4.1, 0IL.15, X6N.16, 01.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.135 2IL.20: 5 residues within 4Å: Chain D: I.135 Ligands: 01.2, GP4.8, 0IL.21, X6N.22 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.135

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

0IL.15: 6 residues within 4Å: Chain C: V.45, F.47, Y.84, F.133 Ligands: GP4.1, 2IL.14 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.45, C:V.45, C:F.47, C:F.133 Salt bridges: A:K.335 0IL.21: 6 residues within 4Å: Chain D: V.45, F.47, Y.84, F.133 Ligands: GP4.8, 2IL.20 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:V.45, D:V.45, D:F.47, D:F.133 Salt bridges: B: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.16: 6 residues within 4Å: Chain A: Q.314, K.335 Chain C: E.104 Ligands: GP4.1, 2IL.14, 01.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Q.314, C:E.104 Salt bridges: A:K.335 X6N.22: 6 residues within 4Å: Chain B: Q.314, K.335 Chain D: E.104 Ligands: 01.2, GP4.8, 2IL.20 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Q.314, B:K.335, B:K.335, D:E.104 Salt bridges: B: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

Toll-like receptor 4: AB
Lymphocyte antigen 96: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Toll-like receptor 4

Lymphocyte antigen 96

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