SMTL ID : 5zsa.1

Crystal structure of monkey TLR7 in complex with IMDQ and UUUUUU

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x U- U- U- U: RNA (5'-R(P*UP*UP*UP*U)-3')(Non-covalent)

U-U-U-U.1: 24 residues within 4Å: Chain A: I.52, H.54, R.75, C.76, V.79, L.83, G.84, S.85, N.88, D.113, E.134, A.135, Q.159, Y.162, R.164, R.445, Y.446, D.447, A.450, R.451, S.452, C.453 Chain B: R.614, K.666 Protein-ligand interaction information (PLIP) not available U-U-U-U.2: 23 residues within 4Å: Chain A: R.614 Chain B: I.52, H.54, R.75, C.76, V.79, L.83, G.84, S.85, N.88, D.113, E.134, A.135, Q.159, Y.162, R.164, R.445, Y.446, D.447, A.450, R.451, S.452, C.453 Protein-ligand interaction information (PLIP) not available

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

NAG-NAG.3: 7 residues within 4Å: Chain A: I.26, N.47, V.70, E.71, K.108, S.109, Q.129 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.108 NAG-NAG.4: 9 residues within 4Å: Chain A: C.161, Y.162, Y.163, P.166, C.167, Y.168, V.169, S.170, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 9 residues within 4Å: Chain B: C.161, Y.162, Y.163, P.166, C.167, Y.168, V.169, S.170, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain B: N.47, V.70, E.71, K.108, S.109, Q.129 No protein-ligand interaction detected (PLIP)

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

NAG.7: 7 residues within 4Å: Chain A: S.407, S.468, C.469, S.479, N.501, Y.524, D.526 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:S.407, A:S.407, A:C.469, A:S.479, A:D.526 Water bridges: A:N.501, A:N.501 NAG.8: 5 residues within 4Å: Chain A: S.537, M.566, N.568, S.591, R.592 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.537, A:S.537, A:R.592 NAG.9: 4 residues within 4Å: Chain A: N.391, S.393, K.396, H.493 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.391, A:K.396, A:K.396 NAG.10: 4 residues within 4Å: Chain A: R.674, R.695, N.698, R.701 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.695, A:R.701 Water bridges: A:R.674 NAG.11: 3 residues within 4Å: Chain A: K.306, G.309, N.339 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain A: E.632, N.657, T.681 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.657 NAG.13: 2 residues within 4Å: Chain A: N.512, S.514 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.514 NAG.19: 7 residues within 4Å: Chain B: S.407, S.468, C.469, S.479, N.501, Y.524, D.526 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:S.407, B:S.407, B:C.469, B:S.479, B:D.526, B:D.526 NAG.20: 6 residues within 4Å: Chain B: S.537, M.566, N.568, K.571, T.590, S.591 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 NAG.21: 2 residues within 4Å: Chain B: N.512, S.514 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.512, B:S.514 NAG.22: 3 residues within 4Å: Chain B: E.632, N.657, T.681 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.632, B:N.657 Water bridges: B:E.603

2 x IDQ: 1-[[4-(aminomethyl)phenyl]methyl]-2-butyl-imidazo[4,5-c]quinolin-4-amine(Non-covalent)

IDQ.14: 13 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: F.329, Q.332, V.333, Y.334, V.359, F.386 Ligands: SO4.18 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:T.510, A:L.535, A:L.535, B:F.329, B:F.329, B:Y.334, B:F.386 Hydrogen bonds: A:D.533, A:T.564 pi-Stacking: B:Y.334, B:F.386, B:F.386 IDQ.23: 15 residues within 4Å: Chain A: N.243, F.327, F.329, Q.332, V.333, Y.334, V.359, F.386 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 Ligands: SO4.26 14 PLIP interactions: 9 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.327, A:F.329, A:F.329, A:Y.334, A:F.386, A:F.386, B:T.510, B:L.535, B:L.535 pi-Stacking: A:Y.334, A:F.386, A:F.386 Hydrogen bonds: B:D.533, B:T.564

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

SO4.15: 4 residues within 4Å: Chain A: L.535, H.536, S.537, T.538 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.537, A:T.538 Salt bridges: A:H.536 SO4.16: 4 residues within 4Å: Chain A: K.364, S.365, N.391, M.394 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.365, A:N.391 Water bridges: A:L.363 Salt bridges: A:K.364 SO4.17: 3 residues within 4Å: Chain A: I.707, Y.729 Ligands: NAG.12 No protein-ligand interaction detected (PLIP) SO4.18: 4 residues within 4Å: Chain A: L.535, H.536 Chain B: Y.334 Ligands: IDQ.14 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.536 SO4.24: 4 residues within 4Å: Chain B: L.535, H.536, S.537, M.566 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 SO4.25: 2 residues within 4Å: Chain B: H.798, T.810 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.798 SO4.26: 4 residues within 4Å: Chain B: T.510, L.535, H.536 Ligands: IDQ.23 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.536 SO4.27: 8 residues within 4Å: Chain B: Y.211, D.233, S.235, H.276, Y.446, D.447, K.448, Y.449 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.447, B:K.448 Water bridges: B:N.212, B:N.212, B:S.235, B:S.235 Salt bridges: B:H.276, B:K.448 SO4.28: 3 residues within 4Å: Chain B: R.335, A.336, S.337 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.336, B:S.337 Salt bridges: B:R.335 SO4.29: 4 residues within 4Å: Chain A: N.529 Chain B: R.531, S.555, H.556 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.555, B:H.556, A:N.529 Water bridges: B:S.555, B:H.556, B:H.556 Salt bridges: B:R.531 SO4.30: 9 residues within 4Å: Chain B: C.161, Y.162, Y.163, D.191, N.192, N.193, N.212, N.213, Y.446 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.163, B:N.193, B:N.212, B:Y.446

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Structural Analyses of Toll-like Receptor 7 Reveal Detailed RNA Sequence Specificity and Recognition Mechanism of Agonistic Ligands. Cell Rep (2018)

Release Date

2019-01-30

Peptides

Toll-like receptor 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Toll-like receptor 7

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