SMTL ID : 3j0a.1

Homology model of human Toll-like receptor 5 fitted into an electron microscopy single particle reconstruction

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

Ligands

14 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.1: 6 residues within 4Å: Chain A: C.14, N.15, L.16, V.19, Q.21, Y.35 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.35, A:Y.35, A:Q.21 Hydrophobic interactions: A:V.19 NAG-FUC.2: 3 residues within 4Å: Chain A: L.23, N.24, E.48 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.48 Hydrophobic interactions: A:L.23 NAG-FUC.3: 5 residues within 4Å: Chain A: V.190, S.191, W.194, I.220, N.223 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.220 Hydrogen bonds: A:D.219 NAG-FUC.4: 5 residues within 4Å: Chain A: N.296, A.298, V.318, N.320, Y.342 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.318 Hydrogen bonds: A:N.320 NAG-FUC.5: 1 residues within 4Å: Chain A: N.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.400 NAG-FUC.6: 7 residues within 4Å: Chain A: N.570, N.573, H.574, L.599, F.600, S.601, L.602 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.574 NAG-FUC.7: 3 residues within 4Å: Chain A: H.574, T.575, N.576 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.574 NAG-FUC.8: 5 residues within 4Å: Chain B: C.14, N.15, V.19, Q.21, Y.35 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.490, B:C.14, B:Y.35 Hydrophobic interactions: B:V.19 NAG-FUC.9: 4 residues within 4Å: Chain B: L.23, N.24, F.46, E.48 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.48, B:N.24 Hydrophobic interactions: B:L.23, B:N.24 NAG-FUC.10: 5 residues within 4Å: Chain B: V.190, S.191, W.194, I.220, N.223 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.194, B:I.220 Hydrogen bonds: B:N.223 NAG-FUC.11: 5 residues within 4Å: Chain B: N.296, Y.299, V.318, N.320, Y.342 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.318 Hydrogen bonds: B:N.320 NAG-FUC.12: 2 residues within 4Å: Chain B: I.380, N.400 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.400 NAG-FUC.13: 4 residues within 4Å: Chain B: N.570, N.573, H.574, L.602 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.570 NAG-FUC.14: 3 residues within 4Å: Chain B: H.574, T.575, N.576 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.574

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, K. et al., Toll-like receptor 5 forms asymmetric dimers in the absence of flagellin. J.Struct.Biol. (2012)

Release Date

2011-12-28

Peptides

Toll-like receptor 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 5