SMTL ID : 5gmg.1

Crystal structure of monkey TLR7 in complex with loxoribine and polyU

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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: 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, R.164, R.445, Y.446, D.447, A.450, R.451, S.452, C.453 Chain B: R.614 Protein-ligand interaction information (PLIP) not available U-U-U-U.2: 24 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, 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

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: 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: 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)

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

NAG.5: 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:E.71, A:S.109 NAG.6: 5 residues within 4Å: Chain A: E.632, D.634, N.657, S.659, T.681 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.634 Hydrogen bonds: A:T.681 NAG.7: 7 residues within 4Å: Chain A: S.468, C.469, S.479, K.480, N.501, Y.524, D.526 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.524, A:D.526 Hydrogen bonds: A:C.469, A:S.479, A:N.501, A:D.526 NAG.10: 4 residues within 4Å: Chain B: S.537, N.568, T.590, S.591 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.537, B:S.537 NAG.11: 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:N.501, B:D.526 NAG.12: 5 residues within 4Å: Chain B: H.24, N.47, V.70, E.71, S.109 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.47, B:E.71, B:S.109, B:S.109

2 x SDL: 2-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7-prop-2-enyl-1~{H}-purine-6,8-dione(Non-covalent)

SDL.8: 12 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: F.329, Q.332, Y.334, V.359, F.386, K.410 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:L.535, B:Y.334 Hydrogen bonds: A:G.562, A:T.564, A:T.564, B:Q.332, B:K.410, B:K.410 Salt bridges: A:D.533 pi-Stacking: B:Y.334, B:F.386, B:F.386 SDL.9: 12 residues within 4Å: Chain A: F.329, Q.332, Y.334, V.359, F.386, K.410 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.334, B:L.535 Hydrogen bonds: A:Q.332, B:G.562, B:T.564, B:T.564, B:T.564 pi-Stacking: A:Y.334, A:F.386, A:F.386 Salt bridges: B:D.533

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 2 residues within 4Å: Chain B: R.674, N.698 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.698 Salt bridges: B:R.674

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, Z. et al., Structural Analysis Reveals that Toll-like Receptor 7 Is a Dual Receptor for Guanosine and Single-Stranded RNA. Immunity (2016)

Release Date

2016-11-02

Peptides

Toll-like receptor 7: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Toll-like receptor 7

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