SMTL ID : 5zsl.1

Crystal structure of monkey TLR7 in complex with GGUUGG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

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

U-U-G-A.1: 22 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, 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 U-U-G-A.2: 22 residues within 4Å: Chain A: I.52, H.54, R.75, C.76, V.79, L.83, G.84, S.85, D.113, E.134, A.135, Q.159, Y.162, Y.163, 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: 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.4: 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.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: 5 residues within 4Å: Chain B: N.47, V.70, E.71, S.109, Q.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.109

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

NAG.7: 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.8: 4 residues within 4Å: Chain A: S.537, M.566, N.568, S.591 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.537, A:S.537 NAG.9: 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.10: 5 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492 Ligands: SO4.15 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.391, A:K.396, A:K.396, A:Q.492 NAG.11: 4 residues within 4Å: Chain A: K.306, G.309, D.310, N.339 No protein-ligand interaction detected (PLIP) NAG.12: 2 residues within 4Å: Chain A: N.512, S.514 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.512, A:S.514 NAG.13: 5 residues within 4Å: Chain A: E.632, N.657, T.681, N.705 Ligands: SO4.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.657 NAG.20: 7 residues within 4Å: Chain B: S.468, C.469, S.479, K.480, N.501, Y.524, D.526 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.524 Hydrogen bonds: B:C.469, B:S.479, B:D.526, B:D.526 NAG.21: 5 residues within 4Å: Chain B: S.537, M.566, N.568, K.571, S.591 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 NAG.22: 2 residues within 4Å: Chain B: N.512, S.514 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.514 NAG.23: 5 residues within 4Å: Chain B: N.391, S.393, K.396, Q.492, H.493 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.391, B:S.393, B:K.396, B:K.396, B:Q.492

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

SO4.14: 4 residues within 4Å: Chain A: H.536, S.537, T.538, M.566 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.537, A:T.538 Salt bridges: A:H.536 SO4.15: 5 residues within 4Å: Chain A: K.364, S.365, N.391, M.394 Ligands: NAG.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.365, A:N.391 SO4.16: 6 residues within 4Å: Chain A: Y.211, D.233, H.276, Y.446, D.447, K.448 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.211, A:D.447, A:K.448 Salt bridges: A:H.276 SO4.17: 4 residues within 4Å: Chain A: N.705, I.707, Y.729 Ligands: NAG.13 No protein-ligand interaction detected (PLIP) SO4.24: 5 residues within 4Å: Chain B: L.535, 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 SO4.25: 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 SO4.26: 9 residues within 4Å: Chain B: Y.211, N.212, 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:N.212, B:D.447, B:K.448 Salt bridges: B:H.276

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)

9K9.18: 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 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.562, A:T.564, A:T.564, A:T.564, B:Y.242, B:Q.332, B:Q.332 Salt bridges: A:D.533 pi-Stacking: B:Y.334, B:F.386, B:F.386 9K9.19: 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 12 PLIP interactions: 5 interactions with chain B, 7 interactions with chain A Hydrogen bonds: B:G.562, B:T.564, B:T.564, B:T.564, A:Q.332, A:Q.332, A:K.388, A:K.410 Salt bridges: B:D.533 pi-Stacking: A:Y.334, A:F.386, A:F.386

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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