SMTL ID : 5zsm.1

Crystal structure of monkey TLR7 in complex with GGUCCC

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x G- U- C- C- C: RNA (5'-R(*GP*UP*CP*CP*C)-3')(Non-covalent)

G-U-C-C-C.1: 26 residues within 4Å: Chain A: H.608, D.610, V.611, 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, Q.159, Y.162, R.164, Q.440, R.445, Y.446, D.447, A.450, R.451, S.452, C.453 Protein-ligand interaction information (PLIP) not available G-U-C-C-C.2: 29 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, Q.440, R.445, Y.446, D.447, K.448, A.450, R.451, S.452, C.453, R.454 Chain B: H.608, D.610, V.611, R.614 Protein-ligand interaction information (PLIP) not available

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.3: 8 residues within 4Å: Chain A: C.161, Y.162, P.166, C.167, Y.168, V.169, S.170, N.193 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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)

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

NAG.5: 5 residues within 4Å: Chain A: S.537, M.566, N.568, K.571, S.591 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.571 Hydrogen bonds: A:S.537, A:S.537, A:K.571 NAG.6: 8 residues within 4Å: Chain A: S.407, S.468, C.469, S.479, K.480, N.501, Y.524, D.526 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.524 Hydrogen bonds: A:S.407, A:S.407, A:C.469, A:S.479, A:N.501, A:D.526 NAG.7: 6 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492, H.493 Ligands: SO4.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.391, A:K.396, A:K.396 NAG.8: 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:N.698, A:R.701 NAG.9: 4 residues within 4Å: Chain A: K.306, G.309, D.310, N.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.306 NAG.10: 1 residues within 4Å: Chain A: N.512 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.514 NAG.11: 4 residues within 4Å: Chain A: N.47, V.70, E.71, S.109 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.47, A:S.109, A:S.109 NAG.12: 4 residues within 4Å: Chain A: E.632, N.657, T.681, N.705 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.657 NAG.17: 4 residues within 4Å: Chain B: S.537, M.566, N.568, S.591 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 NAG.18: 8 residues within 4Å: Chain B: S.468, C.469, S.479, K.480, N.501, S.503, Y.524, D.526 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:C.469, B:S.479, B:N.501, B:D.526, B:D.526 NAG.19: 5 residues within 4Å: Chain B: I.26, N.47, V.70, E.71, S.109 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.26 Hydrogen bonds: B:N.47, B:S.109, B:S.109 NAG.20: 4 residues within 4Å: Chain B: N.391, S.393, K.396, Q.492 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.391, B:K.396, B:K.396 NAG.21: 1 residues within 4Å: Chain B: N.512 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.512

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

SO4.13: 3 residues within 4Å: Chain A: 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 SO4.14: 6 residues within 4Å: Chain A: S.85, K.86, S.87 Chain B: S.641, F.642, K.666 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:S.85, A:K.86, A:S.87, B:S.641, B:S.641 Salt bridges: B:K.666 SO4.15: 6 residues within 4Å: Chain A: L.363, K.364, S.365, N.391, M.394 Ligands: NAG.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.363, A:S.365, A:N.391 SO4.22: 6 residues within 4Å: Chain A: S.641, F.642, K.666 Chain B: S.85, K.86, S.87 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.86, B:S.87, B:S.87, A:S.641 Salt bridges: A:K.666 SO4.23: 4 residues within 4Å: Chain B: H.536, S.537, T.538, M.566 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.537, B:S.537, B:T.538 Salt bridges: B:H.536 SO4.24: 2 residues within 4Å: Chain B: H.798, T.810 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.810 Salt bridges: B:H.798 SO4.25: 8 residues within 4Å: Chain B: Y.211, D.233, S.235, H.276, Y.446, D.447, K.448, Y.449 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.211, B:K.448 Salt bridges: B:H.276, B:K.448 SO4.26: 3 residues within 4Å: Chain B: R.335, A.336, S.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.336, B:S.337 SO4.27: 3 residues within 4Å: Chain B: R.714, K.736, R.762 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.714, B:K.736, B:R.762

2 x 9K9: 2-amino-9-[(2S,3aR,4R,6R,6aR)-2-hydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]-3,9-dihydro-6H-purin-6-one(Non-covalent)

9K9.16: 14 residues within 4Å: Chain A: Y.242, F.329, L.331, Q.332, Y.334, V.359, F.386, K.410 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:G.562, B:T.564, B:T.564, B:T.564, A:Q.332, A:Q.332 Salt bridges: B:D.533 pi-Stacking: A:Y.334, A:F.386, A:F.386 9K9.28: 14 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: Y.242, F.329, L.331, Q.332, Y.334, V.359, F.386, K.410 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:Y.242, B:Q.332, B:Q.332, A:G.562, A:T.564, A:T.564, A:T.564 pi-Stacking: B:Y.334, B:F.386, B:F.386 Water bridges: A:D.533 Salt bridges: A:D.533

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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