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

Crystal structure of the ATP-gated human P2X3 ion channel in the ATP-bound, closed (desensitized) state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

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

GLC-GLC.1: 3 residues within 4Å: Chain A: W.40, H.44, E.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.44 GLC-GLC.15: 3 residues within 4Å: Chain B: W.40, H.44, E.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.44 GLC-GLC.29: 3 residues within 4Å: Chain C: W.40, H.44, E.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.44

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

ATP.2: 15 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 Ligands: EDO.9, NA.13 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:T.171, 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 Water bridges: A:D.157, A:R.280 ATP.16: 15 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 Ligands: EDO.23, NA.27 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:T.171, 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:R.280 ATP.30: 15 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 Ligands: EDO.37, NA.41 13 PLIP interactions: 8 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:T.171, 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 Water bridges: C:R.280

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

NAG.3: 3 residues within 4Å: Chain A: M.165, E.168, N.169 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: L.191, N.193, W.252, D.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.193 NAG.5: 4 residues within 4Å: Chain A: M.102, M.287, N.289, S.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.291 NAG.17: 3 residues within 4Å: Chain B: M.165, E.168, N.169 No protein-ligand interaction detected (PLIP) NAG.18: 4 residues within 4Å: Chain B: L.191, N.193, W.252, D.253 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.193 NAG.19: 4 residues within 4Å: Chain B: M.102, M.287, N.289, S.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.291 NAG.31: 3 residues within 4Å: Chain C: M.165, E.168, N.169 No protein-ligand interaction detected (PLIP) NAG.32: 4 residues within 4Å: Chain C: L.191, N.193, W.252, D.253 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.193 NAG.33: 4 residues within 4Å: Chain C: M.102, M.287, N.289, S.291 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.291

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

EDO.6: 3 residues within 4Å: Chain A: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: G.225, Q.226, D.227 No protein-ligand interaction detected (PLIP) EDO.8: 2 residues within 4Å: Chain A: N.138, S.141 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.138, A:V.142 EDO.9: 7 residues within 4Å: Chain A: S.274, G.276, Y.277, N.278 Chain C: V.60, T.61 Ligands: ATP.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:T.61, A:G.276, A:N.278 EDO.20: 3 residues within 4Å: Chain B: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.21: 3 residues within 4Å: Chain B: G.225, Q.226, D.227 No protein-ligand interaction detected (PLIP) EDO.22: 2 residues within 4Å: Chain B: N.138, S.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.138, B:V.142 EDO.23: 7 residues within 4Å: Chain A: V.60, T.61 Chain B: S.274, G.276, Y.277, N.278 Ligands: ATP.16 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.34: 3 residues within 4Å: Chain C: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.35: 3 residues within 4Å: Chain C: G.225, Q.226, D.227 No protein-ligand interaction detected (PLIP) EDO.36: 2 residues within 4Å: Chain C: N.138, S.141 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.138, C:V.142 EDO.37: 7 residues within 4Å: Chain B: V.60, T.61 Chain C: S.274, G.276, Y.277, N.278 Ligands: ATP.30 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:T.61, C:G.276, C:N.278

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.10: 2 residues within 4Å: Chain A: R.135, E.147 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.135 ACT.11: 7 residues within 4Å: Chain A: K.46, Q.49, V.245, C.246, D.247, N.311, G.313 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.245 Hydrogen bonds: A:N.311, A:G.313 Salt bridges: A:K.46 ACT.24: 2 residues within 4Å: Chain B: R.135, E.147 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.135 ACT.25: 7 residues within 4Å: Chain B: K.46, Q.49, V.245, C.246, D.247, N.311, G.313 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.245 Hydrogen bonds: B:N.311, B:G.313 Salt bridges: B:K.46 ACT.38: 2 residues within 4Å: Chain C: R.135, E.147 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.135 ACT.39: 7 residues within 4Å: Chain C: K.46, Q.49, V.245, C.246, D.247, N.311, G.313 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.245 Hydrogen bonds: C:N.311, C:G.313 Salt bridges: C:K.46

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

NA.12: 1 residues within 4Å: Chain A: D.209 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.209 NA.13: 2 residues within 4Å: Chain A: E.110 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.110 NA.26: 1 residues within 4Å: Chain B: D.209 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.209 NA.27: 2 residues within 4Å: Chain B: E.110 Ligands: ATP.16 No protein-ligand interaction detected (PLIP) NA.40: 1 residues within 4Å: Chain C: D.209 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.209 NA.41: 2 residues within 4Å: Chain C: E.110 Ligands: ATP.30 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.110

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.14: 2 residues within 4Å: Ligands: TRS.28, TRS.42 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: C:S.330, A:S.330, B:S.330 TRS.28: 2 residues within 4Å: Ligands: TRS.14, TRS.42 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:S.330, C:S.330, B:S.330 TRS.42: 2 residues within 4Å: Ligands: TRS.14, TRS.28 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:S.330, B:S.330, 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

2016-10-05

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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