SMTL ID : 8wqt.1

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM1 complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.60 Å

Oligo State

hetero-2-2-mer

Ligands

6 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 C: V.152, N.179, H.203, R.231 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.231 NAG-NAG.2: 6 residues within 4Å: Chain C: S.477, N.499, S.501, D.523 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain C: T.521, D.523, F.545, N.547, V.574 Ligands: NAG-NAG.2, NAG-NAG.2 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.545 Hydrogen bonds: C:T.521 NAG-NAG.4: 4 residues within 4Å: Chain D: V.152, N.179, H.203, R.231 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.231 NAG-NAG.5: 6 residues within 4Å: Chain D: S.477, N.499, S.501, D.523 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain D: T.521, D.523, F.545, N.547, V.574 Ligands: NAG-NAG.5, NAG-NAG.5 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.545 Hydrogen bonds: D:T.521

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

NAG.7: 2 residues within 4Å: Chain A: E.46, N.96 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: D.20, R.114, V.116, N.132 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain B: E.46, N.96 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain B: D.20, R.114, V.116, N.132 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain C: N.147 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: D.24, Y.46, N.50 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: P.8, N.9 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain C: N.467 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: N.212, R.241 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain C: H.278, C.279, N.282 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain D: N.147 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: D.24, Y.46, N.50 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: P.8, N.9 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.467 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain D: N.212, R.241 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: H.278, C.279, N.282 Ligand excluded by PLIP

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

2IL.9: 8 residues within 4Å: Chain A: V.43, L.60, E.74, S.102 Ligands: 2IL.10, GP4.22, 0IL.23, X6Z.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.43, A:L.60 2IL.10: 11 residues within 4Å: Chain A: I.28, V.43, V.45, F.47, F.58, E.74, Y.84, F.86, F.101 Ligands: 2IL.9, X6Z.32 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.28, A:V.43, A:V.45, A:V.45, A:F.47, A:E.74, A:F.86, A:F.101 2IL.13: 8 residues within 4Å: Chain B: V.43, L.60, E.74, S.102 Ligands: 2IL.14, X6Z.21, GP4.30, 0IL.31 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.43, B:L.60 2IL.14: 11 residues within 4Å: Chain B: I.28, V.43, V.45, F.47, F.58, E.74, Y.84, F.86, F.101 Ligands: 2IL.13, X6Z.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.28, B:V.43, B:V.45, B:V.45, B:F.47, B:E.74, B:F.86, B:F.101

2 x X6Z: [(2~{R},3~{S},4~{S},5~{S})-5-methoxy-3,4,6-tris(oxidanyl)oxan-2-yl]methyl dihydrogen phosphate(Non-covalent)

X6Z.21: 5 residues within 4Å: Chain C: Q.314, K.335 Ligands: 2IL.13, 2IL.14, GP4.30 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.314, C:K.335 Salt bridges: C:K.238, C:K.335, C:K.335 X6Z.32: 5 residues within 4Å: Chain D: K.238, K.335 Ligands: 2IL.9, 2IL.10, GP4.22 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.238, D:K.335 Salt bridges: D:K.238, D:K.335, D:K.335

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

GP4.22: 5 residues within 4Å: Chain C: R.409 Chain D: K.335 Ligands: 2IL.9, 0IL.23, X6Z.32 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.409 Hydrogen bonds: D:K.335 GP4.30: 5 residues within 4Å: Chain C: K.335 Chain D: R.409 Ligands: 2IL.13, X6Z.21, 0IL.31 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:K.335 Salt bridges: D:R.409

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

0IL.23: 11 residues within 4Å: Chain A: I.34, I.62, R.72, F.108, Y.113, I.135 Chain C: R.409, E.412, F.413 Ligands: 2IL.9, GP4.22 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:I.34, A:I.62, A:F.108, A:Y.113, A:Y.113, A:I.135, C:F.413, C:F.413 Salt bridges: C:R.409 0IL.31: 10 residues within 4Å: Chain B: I.34, I.62, R.72, F.108, Y.113, I.135 Chain D: R.409, F.413 Ligands: 2IL.13, GP4.30 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.34, B:I.62, B:F.108, B:Y.113, B:Y.113, B:I.135, D:F.413 Salt bridges: D:R.409

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2024-10-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

D
A

Lymphocyte antigen 96

Toll-like receptor 4

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