SMTL ID : 5gmf.2 (1 other biounit)

Crystal structure of monkey TLR7 in complex with guanosine and polyU

Coordinates

PDB Format Compare

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: 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 U-U-U-U.2: 23 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 Protein-ligand interaction information (PLIP) not available

3 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: 6 residues within 4Å: Chain A: K.22, I.26, N.47, V.70, E.71, S.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.22 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)

2 x GMP: GUANOSINE(Non-covalent)

GMP.6: 11 residues within 4Å: Chain A: T.510, D.533, L.535, G.562, I.563, T.564 Chain B: F.329, Y.334, V.359, F.386, K.410 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A pi-Stacking: B:Y.334, B:F.386, B:F.386 Hydrogen bonds: A:T.564, A:T.564, A:T.564 Water bridges: A:D.533 Salt bridges: A:D.533 GMP.12: 11 residues within 4Å: Chain A: F.329, Y.334, V.359, F.386, K.410 Chain B: T.510, D.533, L.535, G.562, I.563, T.564 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.242, B:G.562, B:T.564, B:T.564 pi-Stacking: A:Y.334, A:F.386, A:F.386 Salt bridges: B:D.533

3 x CA: CALCIUM ION(Non-covalent)

CA.7: 1 residues within 4Å: Chain A: D.807 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.807 CA.13: 1 residues within 4Å: Chain B: D.807 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.807 CA.14: 1 residues within 4Å: Chain B: W.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:W.7

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

NAG.8: 8 residues within 4Å: Chain A: S.468, C.469, S.479, K.480, N.501, S.503, 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:N.501, A:D.526, A:D.526 NAG.9: 3 residues within 4Å: Chain A: K.306, R.335, N.339 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.335 NAG.10: 5 residues within 4Å: Chain A: N.391, S.393, K.396, Q.492, H.493 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.391, A:K.396, A:K.396 NAG.11: 3 residues within 4Å: Chain A: N.23, N.44, H.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.23, A:N.44 NAG.15: 8 residues within 4Å: Chain B: S.468, C.469, S.479, K.480, N.501, S.503, 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.16: 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.17: 6 residues within 4Å: Chain B: H.24, 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.18: 4 residues within 4Å: Chain B: N.23, T.43, N.44, H.68 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.23 NAG.19: 3 residues within 4Å: Chain B: K.306, R.335, N.339 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.306, B:R.335, B:N.339

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
B

B
D

Toll-like receptor 7

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