SMTL ID : 8wry.1

Cryo-EM Structure of Mouse TLR4/MD-2/DLAM3 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: 6 residues within 4Å: Chain C: V.152, N.179, S.181, H.203, E.204, R.231 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.231, C:R.231 NAG-NAG.2: 7 residues within 4Å: Chain C: S.477, K.478, N.499, H.502, D.523 Ligands: NAG-NAG.3, NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 8 residues within 4Å: Chain C: T.521, D.523, S.525, F.545, N.547, V.574 Ligands: NAG-NAG.2, NAG-NAG.2 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.545 NAG-NAG.4: 6 residues within 4Å: Chain D: V.152, N.179, S.181, H.203, E.204, R.231 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.231, D:R.231 NAG-NAG.5: 7 residues within 4Å: Chain D: S.477, K.478, N.499, H.502, D.523 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain D: T.521, D.523, S.525, F.545, N.547, V.574 Ligands: NAG-NAG.5, NAG-NAG.5 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.545

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.12: 2 residues within 4Å: Chain B: E.46, N.96 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain B: D.20, R.114, V.116, N.132 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain C: S.146, N.147 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: D.24, Y.46, N.50 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain C: P.8, N.9 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain C: N.467 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain C: N.212, S.213, R.241 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: H.278, C.279, N.282, K.304 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain D: S.146, N.147 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain D: D.24, Y.46, N.50 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain D: P.8, N.9 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain D: N.467 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: N.212, S.213, R.241 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: H.278, C.279, N.282, K.304 Ligand excluded by PLIP

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

2IL.9: 6 residues within 4Å: Chain A: L.60, S.102 Ligands: 0IL.10, 2IL.11, GP4.24, XIQ.31 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.60 2IL.11: 12 residues within 4Å: Chain A: I.28, V.43, V.45, F.47, F.58, E.74, Y.84, F.101, F.133 Chain D: K.238 Ligands: 2IL.9, XIQ.31 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.28, A:V.43, A:V.45, A:F.47, A:F.58, A:F.58, A:E.74, A:F.133 Hydrogen bonds: A:Y.84 Salt bridges: D:K.238 2IL.14: 6 residues within 4Å: Chain B: L.60, S.102 Ligands: 0IL.15, 2IL.16, XIQ.23, GP4.32 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.60 2IL.16: 11 residues within 4Å: Chain B: I.28, V.43, V.45, F.47, F.58, E.74, Y.84, F.101, F.133 Ligands: 2IL.14, XIQ.23 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.28, B:V.43, B:V.45, B:F.47, B:F.58, B:F.58, B:E.74, B:F.133 Hydrogen bonds: B:Y.84 Salt bridges: C:K.238

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

0IL.10: 9 residues within 4Å: Chain A: I.14, I.34, R.72, F.108, Y.113, I.135 Chain C: R.409 Ligands: 2IL.9, GP4.24 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:I.14, A:I.34, A:F.108, A:I.135 Salt bridges: C:R.409 0IL.15: 10 residues within 4Å: Chain B: I.14, I.34, R.72, F.108, Y.113, I.135 Chain D: R.409, F.413 Ligands: 2IL.14, GP4.32 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:I.14, B:I.34, B:F.108, B:I.135, D:F.413 Salt bridges: D:R.409

2 x XIQ: 2-(hydroxymethyl)-5-methoxy-3,6-bis(oxidanyl)pyran-4-one(Post Translational Modification)

XIQ.23: 5 residues within 4Å: Chain B: S.102 Chain C: K.335 Ligands: 2IL.14, 2IL.16, GP4.32 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Salt bridges: C:K.335 Hydrogen bonds: B:S.102 XIQ.31: 5 residues within 4Å: Chain A: S.102 Chain D: K.335 Ligands: 2IL.9, 2IL.11, GP4.24 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.238, A:S.102 Salt bridges: D:K.335

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

GP4.24: 4 residues within 4Å: Chain C: R.409 Ligands: 2IL.9, 0IL.10, XIQ.31 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.314, D:K.335 Salt bridges: C:R.409 GP4.32: 4 residues within 4Å: Chain D: R.409 Ligands: 2IL.14, 0IL.15, XIQ.23 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.388 Salt bridges: D:R.409

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: 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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