SMTL ID : 6ah4.1

Structure of human P2X3 receptor in complex with ATP and Ca2+ ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.30 Å

Oligo State

homo-trimer

Ligands

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

GLC-GLC.1: 2 residues within 4Å: Chain A: H.44, E.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 GLC-GLC.2: 2 residues within 4Å: Chain A: D.249, K.314 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.314 GLC-GLC.3: 2 residues within 4Å: Chain B: H.44, E.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.45 GLC-GLC.4: 2 residues within 4Å: Chain B: D.249, K.314 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.249, B:D.249, B:K.314 GLC-GLC.5: 5 residues within 4Å: Chain B: V.50, I.318 Chain C: W.40, H.44, E.45 No protein-ligand interaction detected (PLIP) GLC-GLC.6: 3 residues within 4Å: Chain C: D.249, K.250, K.314 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.314

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Covalent)

ATP.7: 14 residues within 4Å: Chain A: K.62, V.63, K.64, T.171, F.173, M.199, I.214 Chain B: D.157, V.273, S.274, N.278, R.280, K.298 Ligands: CA.18 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:K.62, A:T.171, A:F.173, B:N.278 Salt bridges: A:K.62, A:K.62, A:K.62, A:K.64, A:K.64, B:R.280, B:K.298, B:K.298 pi-Cation interactions: A:K.64 ATP.8: 15 residues within 4Å: Chain A: D.157, 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, I.214 Ligands: CA.12 12 PLIP interactions: 4 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:N.278, C:K.62, C:T.171, C:F.173 Salt bridges: A:R.280, A:K.298, A:K.298, C:K.62, C:K.62, C:K.62, C:K.64 pi-Cation interactions: C:K.64 ATP.17: 13 residues within 4Å: Chain B: K.62, K.64, T.171, F.173, M.199, I.214 Chain C: D.157, V.273, S.274, N.278, R.280, K.298 Ligands: CA.23 14 PLIP interactions: 7 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:K.62, B:T.171, B:F.173, C:D.157, C:N.278 Salt bridges: B:K.62, B:K.62, B:K.62, B:K.64, C:R.280, C:R.280, C:K.298, C:K.298, C:K.298

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

NAG.9: 4 residues within 4Å: Chain A: M.165, E.166, N.169 Chain B: L.126 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.165 Hydrogen bonds: A:N.169 NAG.10: 1 residues within 4Å: Chain A: N.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.193 NAG.13: 3 residues within 4Å: Chain B: M.165, E.166, N.169 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.165 Hydrogen bonds: B:N.169 NAG.14: 2 residues within 4Å: Chain B: N.193, D.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.193, B:D.253 NAG.15: 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.19: 4 residues within 4Å: Chain A: L.126 Chain C: M.165, E.168, N.169 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.168 Hydrogen bonds: C:N.169 NAG.20: 4 residues within 4Å: Chain C: L.191, N.193, D.198, D.253 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.193, C:D.253 NAG.21: 3 residues within 4Å: Chain C: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.289, C:S.291, C:S.291

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

EDO.11: 3 residues within 4Å: Chain A: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.16: 2 residues within 4Å: Chain B: N.100, M.287 No protein-ligand interaction detected (PLIP) EDO.22: 4 residues within 4Å: Chain C: N.100, M.102, M.287, Y.293 No protein-ligand interaction detected (PLIP)

3 x CA: CALCIUM ION(Non-covalent)

CA.12: 2 residues within 4Å: Chain A: D.157 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.157 CA.18: 2 residues within 4Å: Chain B: D.157 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.157 CA.23: 2 residues within 4Å: Chain C: D.157 Ligands: ATP.17 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Molecular mechanisms of human P2X3 receptor channel activation and modulation by divalent cation bound ATP. Elife (2019)

Release Date

2019-06-12

Peptides

P2X purinoceptor 3: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

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

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