SMTL ID : 6ah5.1

Structure of human P2X3 receptor in complex with ATP and Mg2+ ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.82 Å

Oligo State

homo-trimer

Ligands

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

GLC-GLC.1: 5 residues within 4Å: Chain A: H.44, E.45 Chain C: V.50, N.316, I.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.45 GLC-GLC.2: 1 residues within 4Å: Chain A: D.249 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.314 GLC-GLC.3: 5 residues within 4Å: Chain B: V.50, I.318 Chain C: W.40, H.44, E.45 No protein-ligand interaction detected (PLIP)

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

ATP.4: 14 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, F.173, M.199, I.214 Ligands: MG.9 12 PLIP interactions: 8 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:K.62, 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.8: 15 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, N.278, R.280, K.298 Ligands: MG.15 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.14: 14 residues within 4Å: Chain B: K.62, V.63, K.64, T.171, F.173, M.199, I.214 Chain C: D.157, S.274, G.276, N.278, R.280, K.298 Ligands: MG.20 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:K.62, 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: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.5: 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.6: 3 residues within 4Å: Chain A: N.193, D.198, F.211 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.193 NAG.10: 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.11: 4 residues within 4Å: Chain B: L.191, N.193, D.198, D.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.193, B:D.253 NAG.12: 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.16: 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.17: 3 residues within 4Å: Chain C: L.191, N.193, D.198 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.193 NAG.18: 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.7: 1 residues within 4Å: Chain A: N.100 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100 EDO.13: 2 residues within 4Å: Chain B: N.100, M.287 No protein-ligand interaction detected (PLIP) EDO.19: 3 residues within 4Å: Chain C: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 2 residues within 4Å: Chain A: D.157 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.157 MG.15: 2 residues within 4Å: Chain B: D.157 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.157 MG.20: 2 residues within 4Å: Chain C: D.157 Ligands: ATP.14 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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