SMTL ID : 7mlm.1 (1 other biounit)

Crystal structure of mouse TLR4/MD-2 in complex with sulfatides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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.1: 3 residues within 4Å: Chain A: N.220, H.244, R.272 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.272, A:R.272 NAG-NAG.10: 3 residues within 4Å: Chain C: N.220, H.244, R.272 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.272, C:R.272

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

NAG-NAG-NAG.2: 4 residues within 4Å: Chain A: Q.203, P.229, N.253, R.282 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.11: 4 residues within 4Å: Chain C: Q.203, P.229, N.253, R.282 No protein-ligand interaction detected (PLIP)

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

NAG.3: 3 residues within 4Å: Chain A: T.485, N.508, T.510 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.485 Hydrogen bonds: A:N.508, A:T.510 NAG.4: 6 residues within 4Å: Chain A: S.518, K.519, L.538, N.540, S.542, W.588 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.518, A:S.542 Water bridges: A:S.542, A:W.588 NAG.7: 4 residues within 4Å: Chain B: H.85, E.87, N.137, S.139 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.87, B:S.139, B:S.139 NAG.8: 4 residues within 4Å: Chain B: C.60, D.61, R.155, N.173 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.61 Water bridges: B:S.58 NAG.12: 3 residues within 4Å: Chain C: T.485, N.508, T.510 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.485 Hydrogen bonds: C:N.508, C:T.510 NAG.13: 6 residues within 4Å: Chain C: S.518, K.519, L.538, N.540, S.542, W.588 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.518, C:S.542 Water bridges: C:S.542, C:W.588 NAG.16: 4 residues within 4Å: Chain D: H.85, E.87, N.137, S.139 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:H.85, D:E.87, D:S.139, D:S.139 NAG.17: 4 residues within 4Å: Chain D: C.60, D.61, R.155, N.173 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.61 Water bridges: D:S.58

6 x ZKM: N-[(1S,2R,3E)-2-hydroxy-1-{[(3-O-sulfo-beta-D-galactopyranosyl)oxy]methyl}heptadec-3-en-1-yl]-hexadecanamide(Non-covalent)

ZKM.5: 19 residues within 4Å: Chain A: R.353, M.374, R.396 Chain B: L.101, I.103, V.105, L.110, R.113, E.115, I.147, F.149, P.150, Y.154 Chain C: S.429, R.450, F.454, S.455 Ligands: ZKM.6, ZKM.9 11 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: B:L.101, B:I.103, B:V.105, B:I.147, B:F.149, B:P.150, B:Y.154, B:Y.154, C:F.454 Hydrogen bonds: A:M.374 Salt bridges: A:R.396 ZKM.6: 20 residues within 4Å: Chain A: K.279, Q.355 Chain B: I.69, V.86, F.88, L.97, F.99, E.115, L.117, Y.125, F.127, I.140, P.141, F.142, S.143, A.158, L.172, F.174 Ligands: ZKM.5, ZKM.9 21 PLIP interactions: 4 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:K.279, A:K.279, A:Q.355, B:S.143, B:S.143 Water bridges: A:K.279 Hydrophobic interactions: B:I.69, B:V.86, B:F.88, B:L.97, B:F.99, B:F.99, B:F.99, B:L.117, B:L.117, B:F.127, B:I.140, B:F.142, B:A.158, B:L.172, B:F.174 ZKM.9: 18 residues within 4Å: Chain B: I.69, S.70, S.71, I.75, L.77, V.84, F.142, F.144, I.147, F.149, C.156, F.174 Chain C: K.383, S.402, G.403, S.429 Ligands: ZKM.5, ZKM.6 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.69, B:L.77, B:V.84, B:V.84, B:F.142, B:F.144, B:F.144, B:F.144, B:I.147, B:F.149, B:F.174, B:F.174 Hydrogen bonds: C:S.402, C:S.429 Salt bridges: C:K.383 ZKM.14: 19 residues within 4Å: Chain A: S.429, R.450, F.454, S.455 Chain C: R.353, M.374, R.396 Chain D: L.101, I.103, V.105, L.110, R.113, E.115, I.147, F.149, P.150, Y.154 Ligands: ZKM.15, ZKM.18 11 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: D:L.101, D:I.103, D:V.105, D:I.147, D:F.149, D:P.150, D:Y.154, D:Y.154, A:F.454 Hydrogen bonds: C:M.374 Salt bridges: C:R.396 ZKM.15: 20 residues within 4Å: Chain C: K.279, Q.355 Chain D: I.69, V.86, F.88, L.97, F.99, E.115, L.117, Y.125, F.127, I.140, P.141, F.142, S.143, A.158, L.172, F.174 Ligands: ZKM.14, ZKM.18 21 PLIP interactions: 4 interactions with chain C, 17 interactions with chain D Hydrogen bonds: C:K.279, C:K.279, C:Q.355, D:S.143, D:S.143 Water bridges: C:K.279 Hydrophobic interactions: D:I.69, D:V.86, D:F.88, D:L.97, D:F.99, D:F.99, D:F.99, D:L.117, D:L.117, D:F.127, D:I.140, D:F.142, D:A.158, D:L.172, D:F.174 ZKM.18: 18 residues within 4Å: Chain A: K.383, S.402, G.403, S.429 Chain D: I.69, S.70, S.71, I.75, L.77, V.84, F.142, F.144, I.147, F.149, C.156, F.174 Ligands: ZKM.14, ZKM.15 15 PLIP interactions: 12 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:I.69, D:L.77, D:V.84, D:V.84, D:F.142, D:F.144, D:F.144, D:F.144, D:I.147, D:F.149, D:F.174, D:F.174 Hydrogen bonds: A:S.402, A:S.429 Salt bridges: A:K.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, L. et al., Sulfatides are endogenous ligands for the TLR4-MD-2 complex. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-07-28

Peptides

Toll-like receptor 4,Variable lymphocyte receptor B: AC
Lymphocyte antigen 96: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
C

D
C

Toll-like receptor 4,Variable lymphocyte receptor B

Lymphocyte antigen 96

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