SMTL ID : 5svl.2 (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 ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: D.157, V.273, S.274, P.275, N.278, R.280, K.298 Chain B: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Ligands: EDO.6, NA.8 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.62, B:K.64, B:T.171, B:F.173, A:N.278 Water bridges: B:K.64, A:D.157, A:R.280 Salt bridges: B:K.62, B:K.62, B:K.62, B:K.64, A:R.280, A:K.298, A:K.298 pi-Cation interactions: B:K.64 ATP.9: 17 residues within 4Å: Chain B: D.157, V.273, S.274, P.275, 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.14, NA.16 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain C Hydrogen bonds: B:N.278, C:K.62, C:K.64, C:T.171, C:F.173 Water bridges: B:D.157, B:R.280, C:K.64 Salt bridges: B:R.280, B:K.298, B:K.298, C:K.62, C:K.62, C:K.62, C:K.64 pi-Cation interactions: C:K.64 ATP.17: 17 residues within 4Å: Chain A: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain C: D.157, V.273, S.274, P.275, N.278, R.280, K.298 Ligands: EDO.22, NA.24 16 PLIP interactions: 6 interactions with chain C, 10 interactions with chain A Hydrogen bonds: C:N.278, A:K.62, A:K.64, A:T.171, A:F.173 Water bridges: C:D.157, C:R.280, A:K.64 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.2: 4 residues within 4Å: Chain A: M.165, E.166, N.169, R.216 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.166 NAG.3: 5 residues within 4Å: Chain A: L.191, N.193, F.211, D.253, I.256 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.193, A:D.253 NAG.4: 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.10: 4 residues within 4Å: Chain B: M.165, E.166, N.169, R.216 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.166 NAG.11: 5 residues within 4Å: Chain B: L.191, N.193, F.211, D.253, I.256 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.289, B:S.291, 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 Hydrophobic interactions: C:E.166 NAG.19: 5 residues within 4Å: Chain C: L.191, N.193, F.211, D.253, I.256 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.193, C:D.253 NAG.20: 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

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

EDO.5: 3 residues within 4Å: Chain A: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: G.276, Y.277, N.278 Chain B: V.60, T.61, K.62 Ligands: ATP.1 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.276, A:N.278, B:T.61 EDO.13: 3 residues within 4Å: Chain B: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.14: 7 residues within 4Å: Chain B: G.276, Y.277, N.278 Chain C: V.60, T.61, K.62 Ligands: ATP.9 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.276, B:N.278, C:T.61 EDO.21: 3 residues within 4Å: Chain C: N.100, M.102, M.287 No protein-ligand interaction detected (PLIP) EDO.22: 7 residues within 4Å: Chain A: V.60, T.61, K.62 Chain C: G.276, Y.277, N.278 Ligands: ATP.17 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.61, C:G.276, C:N.278

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

ACT.7: 5 residues within 4Å: Chain A: F.204, P.206, P.257, K.258, Y.259 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.206 Hydrogen bonds: A:Y.259 Salt bridges: A:K.258 ACT.15: 5 residues within 4Å: Chain B: F.204, P.206, P.257, K.258, Y.259 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:P.206 Hydrogen bonds: B:Y.259 Salt bridges: B:K.258 ACT.23: 5 residues within 4Å: Chain C: F.204, P.206, P.257, K.258, Y.259 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:P.206 Hydrogen bonds: C:Y.259 Salt bridges: C:K.258

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

NA.8: 2 residues within 4Å: Chain A: D.157 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.157 NA.16: 2 residues within 4Å: Chain B: D.157 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.157 NA.24: 2 residues within 4Å: Chain C: D.157 Ligands: ATP.17 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.157, C:D.157

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
B

B
B

C
B

Membrane

We predict this structure to be a membrane protein.
Show / Hide

P2X purinoceptor 3

Related Entries With Identical Sequence