SMTL ID : 4z0c.1

Crystal structure of TLR13-ssRNA13 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

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: 8 residues within 4Å: Chain A: H.15, I.19, H.39, N.41, T.43, D.63, R.65 Chain C: A.6 28 PLIP interactions: 25 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.10, A:H.15, A:R.20, A:E.92, A:K.579, A:R.609, A:E.611, A:R.635, B:E.511, B:E.511 Water bridges: A:Y.9, A:Y.9, A:R.20, A:K.579, A:R.609, A:R.609, A:R.609, A:R.635, A:R.635 Salt bridges: A:R.20, A:R.609, A:E.611, A:R.635, A:R.635 pi-Stacking: A:Y.9, A:Y.9, A:W.68 Hydrophobic interactions: B:E.511 NAG-NAG.2: 6 residues within 4Å: Chain A: E.187, S.210, R.211, N.232, D.255, V.285 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: R.304, P.328, S.329, N.353 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain B: H.15, L.17, I.19, H.39, N.41, R.65 Chain D: A.6 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.65, B:R.65 NAG-NAG.5: 5 residues within 4Å: Chain B: R.139, T.164, N.165, R.211 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain B: E.187, S.210, R.211, N.232, D.255, V.285 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.234

20 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.7: 1 residues within 4Å: Chain A: N.57 Ligand excluded by PLIP NAG.8: 6 residues within 4Å: Chain A: W.72, K.73, I.74, I.95, S.97, N.99 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: S.138, R.139, N.165, R.211 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: H.183, N.206, K.229, S.230 Ligand excluded by PLIP NAG.11: 7 residues within 4Å: Chain A: L.261, R.262, G.264, H.265, N.289, S.314, D.315 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: Y.318, N.320, D.321 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: N.345, D.369, F.370, S.373 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: G.551, S.552, I.575, N.576 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.25, E.28, V.49 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.57 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: S.59, A.60, E.83, N.84 Ligand excluded by PLIP NAG.18: 6 residues within 4Å: Chain B: W.72, K.73, I.74, I.95, S.97, N.99 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain B: H.173, N.195, S.197, N.219 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: H.183, N.206, K.229, S.230 Ligand excluded by PLIP NAG.21: 7 residues within 4Å: Chain B: L.261, R.262, G.264, H.265, N.289, S.314, D.315 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain B: Y.318, N.320, D.321 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain B: N.345, R.346, D.369, F.370 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: R.304, S.329, N.353 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: G.551, S.552, N.576 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.25, E.28, V.49 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, W. et al., Structural basis for specific recognition of single-stranded RNA by Toll-like receptor 13. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-10-07

Peptides

Toll-like receptor 13: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Toll-like receptor 13