SMTL ID : 5hdh.1

Crystal structure of human TLR8 with an uncleaved Z-loop

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 13 residues within 4Å: Chain A: K.200, F.202, S.204, L.224, D.226, S.228, Y.265, N.267, D.291, S.439, N.440, F.441, Y.442 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.224, A:Y.265 Hydrogen bonds: A:K.200

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

NAG-NAG.2: 7 residues within 4Å: Chain A: I.449, K.450, S.463, N.485, Y.508, D.510, N.513 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain A: K.450, Q.452, Y.508, D.534, V.562, N.564, E.586, V.588 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.452, A:K.450, A:Q.452, A:Y.508 Hydrophobic interactions: A:Y.508

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

NAG.4: 4 residues within 4Å: Chain A: K.217, I.220, Q.258, N.259 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.220 Hydrogen bonds: A:K.217 NAG.5: 3 residues within 4Å: Chain A: R.344, P.368, N.369 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.369 Water bridges: A:N.369, A:N.369 NAG.6: 4 residues within 4Å: Chain A: E.358, Q.362, M.365, N.390 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.362, A:Q.362, A:M.365, A:N.390 NAG.7: 3 residues within 4Å: Chain A: S.496, N.520, S.522 No protein-ligand interaction detected (PLIP) NAG.8: 3 residues within 4Å: Chain A: T.525, Q.555, N.556 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.555 NAG.9: 4 residues within 4Å: Chain A: K.582, S.583, V.585, N.614 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.10: 3 residues within 4Å: Chain A: K.651, K.673, R.697 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.651, A:K.673, A:R.697 SO4.11: 4 residues within 4Å: Chain A: F.255, Q.258, K.282, N.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.258, A:N.283 Salt bridges: A:K.282 SO4.12: 1 residues within 4Å: Chain A: K.339 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.339

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.13: 4 residues within 4Å: Chain A: R.264, H.286, K.288, R.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.312 Salt bridges: A:R.264, A:K.288, A:R.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanji, H. et al., Autoinhibition and relief mechanism by the proteolytic processing of Toll-like receptor 8. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-03-09

Peptides

Toll-like receptor 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Toll-like receptor 8