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

Anomalous sulfur signal reveals the position of agonist 2-methylthio-ATP bound to the ATP-gated human P2X3 ion channel in the desensitized state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-trimer

Ligands

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: D.157, V.273, S.274, P.275, N.278, R.280, K.298 Chain C: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Ligands: NA.5, EDO.6 13 PLIP interactions: 9 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:K.62, C:K.64, C:T.171, C:F.173, A:N.278 Salt bridges: C:K.62, C:K.62, C:K.62, C:K.64, A:R.280, A:K.298, A:K.298 pi-Cation interactions: C:K.64 ATP.7: 17 residues within 4Å: Chain A: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain B: D.157, V.273, S.274, P.275, N.278, R.280, K.298 Ligands: NA.11, EDO.12 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.62, A:K.64, A:T.171, A:F.173, B:N.278 Salt bridges: A:K.62, A:K.62, A:K.62, A:K.64, B:R.280, B:K.298, B:K.298 pi-Cation interactions: A:K.64 ATP.13: 17 residues within 4Å: Chain B: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain C: D.157, V.273, S.274, P.275, N.278, R.280, K.298 Ligands: NA.17, EDO.18 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.62, B:K.64, B:T.171, B:F.173, C:N.278 Salt bridges: B:K.62, B:K.62, B:K.62, B:K.64, C:R.280, C:K.298, C:K.298 pi-Cation interactions: B:K.64

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

NAG.2: 4 residues within 4Å: Chain A: M.165, E.166, N.169, R.216 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.166 Hydrogen bonds: A:N.169, A:R.216 NAG.3: 5 residues within 4Å: Chain A: L.191, N.193, F.211, D.253, I.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.193, A:D.253 NAG.4: 3 residues within 4Å: Chain A: M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.289, A:S.291 NAG.8: 4 residues within 4Å: Chain B: M.165, E.166, N.169, R.216 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.166 Hydrogen bonds: B:N.169, B:R.216 NAG.9: 5 residues within 4Å: Chain B: L.191, N.193, F.211, D.253, I.256 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.193, B:D.253 NAG.10: 3 residues within 4Å: Chain B: M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.289, B:S.291 NAG.14: 4 residues within 4Å: Chain C: M.165, E.166, N.169, R.216 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.166 Hydrogen bonds: C:N.169, C:R.216 NAG.15: 5 residues within 4Å: Chain C: L.191, N.193, F.211, D.253, I.256 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.193, C:D.253 NAG.16: 3 residues within 4Å: Chain C: M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.289, C:S.291

3 x NA: SODIUM ION(Non-functional Binders)

NA.5: 2 residues within 4Å: Chain A: D.157 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.157 NA.11: 2 residues within 4Å: Chain B: D.157 Ligands: ATP.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.157, B:D.157 NA.17: 2 residues within 4Å: Chain C: D.157 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.157

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 10 residues within 4Å: Chain A: S.274, G.276, Y.277, N.278 Chain C: V.60, T.61, K.62, F.173, K.175 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.276, A:N.278, C:T.61 EDO.12: 10 residues within 4Å: Chain A: V.60, T.61, K.62, F.173, K.175 Chain B: S.274, G.276, Y.277, N.278 Ligands: ATP.7 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.276, B:N.278, A:T.61 EDO.18: 10 residues within 4Å: Chain B: V.60, T.61, K.62, F.173, K.175 Chain C: S.274, G.276, Y.277, N.278 Ligands: ATP.13 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.61, C:G.276, C:N.278

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mansoor, S.E. et al., X-ray structures define human P2X3 receptor gating cycle and antagonist action. Nature (2016)

Release Date

2016-09-28

Peptides

P2X purinoceptor 3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor 3

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