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

Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, open state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-trimer

Ligands

6 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.1: 5 residues within 4Å: Chain A: W.40, H.44, E.45 Chain B: V.50, N.316 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 GLC-GLC.2: 3 residues within 4Å: Chain A: Y.48, D.249, F.315 No protein-ligand interaction detected (PLIP) GLC-GLC.8: 5 residues within 4Å: Chain B: W.40, H.44, E.45 Chain C: V.50, N.316 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.44, B:E.45 GLC-GLC.9: 3 residues within 4Å: Chain B: Y.48, D.249, F.315 No protein-ligand interaction detected (PLIP) GLC-GLC.15: 5 residues within 4Å: Chain A: V.50, N.316 Chain C: W.40, H.44, E.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.45 GLC-GLC.16: 3 residues within 4Å: Chain C: Y.48, D.249, F.315 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.249

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

ATP.3: 14 residues within 4Å: Chain A: V.273, S.274, N.278, R.280, K.298 Chain B: K.62, V.63, K.64, T.171, I.172, F.173, M.199, R.203, I.214 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:N.278, B:K.62, B:T.171, B:F.173 Salt bridges: A:R.280, A:K.298, A:K.298, B:K.62, B:K.62, B:K.62, B:K.64 pi-Cation interactions: B:K.64 ATP.10: 14 residues within 4Å: Chain B: V.273, S.274, N.278, R.280, K.298 Chain C: K.62, V.63, K.64, T.171, I.172, F.173, M.199, R.203, I.214 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.62, C:T.171, C:F.173, B:N.278 Salt bridges: C:K.62, C:K.62, C:K.62, C:K.64, B:R.280, B:K.298, B:K.298 pi-Cation interactions: C:K.64 ATP.17: 14 residues within 4Å: Chain A: K.62, V.63, K.64, T.171, I.172, F.173, M.199, R.203, I.214 Chain C: V.273, S.274, N.278, R.280, K.298 12 PLIP interactions: 4 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:N.278, A:K.62, A:T.171, A:F.173 Salt bridges: C:R.280, C:K.298, C:K.298, A:K.62, A:K.62, A:K.62, A:K.64 pi-Cation interactions: A:K.64

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

NAG.4: 4 residues within 4Å: Chain A: M.165, E.166, N.169, R.216 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 NAG.5: 5 residues within 4Å: Chain A: L.191, N.193, F.211, D.253, I.256 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.193 NAG.6: 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.11: 4 residues within 4Å: Chain B: M.165, E.166, N.169, R.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.169 NAG.12: 5 residues within 4Å: Chain B: L.191, N.193, F.211, D.253, I.256 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.193 NAG.13: 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.18: 4 residues within 4Å: Chain C: M.165, E.166, N.169, R.216 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.169 NAG.19: 5 residues within 4Å: Chain C: L.191, N.193, F.211, D.253, I.256 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.193 NAG.20: 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: N.100, M.102, M.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100 EDO.14: 3 residues within 4Å: Chain B: N.100, M.102, M.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100 EDO.21: 3 residues within 4Å: Chain C: N.100, M.102, M.287 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.100

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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