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

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

Coordinates

PDB Format

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: 4 residues within 4Å: Chain A: W.40, H.44, E.45 Chain C: I.318 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.45, C:N.316 GLC-GLC.2: 2 residues within 4Å: Chain A: D.249, K.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.249, A:K.314 GLC-GLC.10: 4 residues within 4Å: Chain A: I.318 Chain B: W.40, H.44, E.45 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.45, A:N.316 GLC-GLC.11: 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.19: 4 residues within 4Å: Chain B: I.318 Chain C: W.40, H.44, E.45 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.316, C:E.45 GLC-GLC.20: 2 residues within 4Å: Chain C: D.249, K.314 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.249, C:K.314

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

ATP.3: 13 residues within 4Å: Chain A: 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 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain C Hydrogen bonds: A:N.278, C:K.62, C:T.171, C:F.173 Water bridges: A:D.157, A:K.298 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.12: 13 residues within 4Å: Chain A: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain B: V.273, S.274, N.278, R.280, K.298 14 PLIP interactions: 8 interactions with chain A, 6 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, B:R.280, B:K.298, B:K.298 pi-Cation interactions: A:K.64 Water bridges: B:D.157, B:K.298 ATP.21: 13 residues within 4Å: Chain B: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain C: V.273, S.274, N.278, R.280, K.298 14 PLIP interactions: 6 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:N.278, B:K.62, B:T.171, B:F.173 Water bridges: C:D.157, C:K.298 Salt bridges: C:R.280, C:K.298, C:K.298, B:K.62, B:K.62, B:K.62, B:K.64 pi-Cation interactions: B:K.64

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

NAG.4: 3 residues within 4Å: Chain A: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 NAG.5: 4 residues within 4Å: Chain A: L.191, N.193, W.252, D.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.193, A:D.253 NAG.6: 3 residues within 4Å: Chain A: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.289, A:S.291, A:S.291 NAG.7: 6 residues within 4Å: Chain A: N.138, S.140, S.141, V.142, L.143, R.144 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.144 Hydrogen bonds: A:S.140 NAG.13: 3 residues within 4Å: Chain B: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.169 NAG.14: 4 residues within 4Å: Chain B: L.191, N.193, W.252, D.253 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.193, B:D.253, B:D.253 NAG.15: 3 residues within 4Å: Chain B: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.289, B:S.291, B:S.291 NAG.16: 6 residues within 4Å: Chain B: N.138, S.140, S.141, V.142, L.143, R.144 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:R.144 Hydrogen bonds: B:S.140 NAG.22: 3 residues within 4Å: Chain C: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.169 NAG.23: 4 residues within 4Å: Chain C: L.191, N.193, W.252, D.253 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.193, C:D.253, C:D.253 NAG.24: 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 NAG.25: 6 residues within 4Å: Chain C: N.138, S.140, S.141, V.142, L.143, R.144 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:R.144 Hydrogen bonds: C:S.140

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

EDO.8: 3 residues within 4Å: Chain A: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.17: 3 residues within 4Å: Chain B: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.26: 3 residues within 4Å: Chain C: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP)

3 x MHA: (CARBAMOYLMETHYL-CARBOXYMETHYL-AMINO)-ACETIC ACID(Non-covalent)

MHA.9: 8 residues within 4Å: Chain A: T.329, S.330 Chain B: T.329, S.330 Chain C: T.329, S.330 Ligands: MHA.18, MHA.27 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.330 MHA.18: 8 residues within 4Å: Chain A: T.329, S.330 Chain B: T.329, S.330 Chain C: T.329, S.330 Ligands: MHA.9, MHA.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.330 MHA.27: 8 residues within 4Å: Chain A: T.329, S.330 Chain B: T.329, S.330 Chain C: T.329, S.330 Ligands: MHA.9, MHA.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.330

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
A

B
A

C
A

Membrane

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

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