SMTL ID : 8wta.1

Cryo-EM Structure of Human TLR4/MD-2/DLAM3 Complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-2-2-mer

Ligands

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: N.500, S.502, V.522, D.524 Ligands: NAG-NAG-BMA.2, NAG-NAG-BMA.2 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: V.522, F.547, L.548, N.549, V.576 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 6 residues within 4Å: Chain D: N.500, S.502, V.522, D.524 Ligands: NAG-NAG-BMA.6, NAG-NAG-BMA.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 7 residues within 4Å: Chain D: V.522, F.547, L.548, N.549, V.576 Ligands: NAG-NAG-BMA.5, NAG-NAG-BMA.5 No protein-ligand interaction detected (PLIP)

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.3: 2 residues within 4Å: Chain B: N.8, S.13 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: N.8, S.13 No protein-ligand interaction detected (PLIP)

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

NAG.7: 1 residues within 4Å: Chain A: N.179 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: S.445, N.471 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.445 NAG.10: 2 residues within 4Å: Chain B: F.46, N.96 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.46 Hydrogen bonds: B:N.96 NAG.15: 2 residues within 4Å: Chain C: F.46, N.96 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.46 Hydrogen bonds: C:N.96 NAG.20: 1 residues within 4Å: Chain D: N.179 No protein-ligand interaction detected (PLIP) NAG.21: 2 residues within 4Å: Chain D: S.445, N.471 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.445

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

GP4.9: 5 residues within 4Å: Chain A: K.315, K.336 Ligands: 0IL.12, XIQ.13, 2IL.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.238 Salt bridges: A:K.315, A:K.336 GP4.22: 5 residues within 4Å: Chain D: K.315, K.336 Ligands: 0IL.17, XIQ.18, 2IL.19 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:K.315, D:K.336

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

2IL.11: 8 residues within 4Å: Chain B: F.103, K.104, I.106, F.108, Y.113, I.135 Ligands: XIQ.13, 2IL.14 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.103, B:F.108, B:Y.113, B:I.135 Hydrogen bonds: B:K.104 2IL.14: 9 residues within 4Å: Chain B: V.30, I.34, L.60, E.74, C.115 Ligands: GP4.9, 2IL.11, 0IL.12, XIQ.13 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.30, B:I.34, B:L.60 2IL.16: 8 residues within 4Å: Chain C: F.103, K.104, I.106, F.108, Y.113, I.135 Ligands: XIQ.18, 2IL.19 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.103, C:F.108, C:Y.113, C:I.135 Hydrogen bonds: C:K.104 2IL.19: 9 residues within 4Å: Chain C: V.30, I.34, L.60, E.74, C.115 Ligands: 2IL.16, 0IL.17, XIQ.18, GP4.22 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.30, C:I.34, C:L.60

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

0IL.12: 7 residues within 4Å: Chain B: I.28, L.43, I.45, Y.47, Y.84 Ligands: GP4.9, 2IL.14 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.28, B:L.43, B:I.45, B:Y.47 0IL.17: 7 residues within 4Å: Chain C: I.28, L.43, I.45, Y.47, Y.84 Ligands: 2IL.19, GP4.22 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:I.28, C:L.43, C:I.45, C:Y.47

2 x XIQ: 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one(Non-covalent)

XIQ.13: 6 residues within 4Å: Chain B: S.102, F.103, K.104 Ligands: GP4.9, 2IL.11, 2IL.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.104 XIQ.18: 6 residues within 4Å: Chain C: S.102, F.103, K.104 Ligands: 2IL.16, 2IL.19, GP4.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.104

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fu, Y. et al., Structure 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: AD
Lymphocyte antigen 96: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

B
C

C
D

Toll-like receptor 4

Lymphocyte antigen 96

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