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

Crystal structure of the ATP-gated human P2X3 ion channel bound to agonist 2-methylthio-ATP in the desensitized state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.09 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: M.165, E.168, N.169 Chain B: P.123 No protein-ligand interaction detected (PLIP) NAG.2: 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.3: 3 residues within 4Å: Chain A: M.287, N.289, S.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.291 NAG.8: 4 residues within 4Å: Chain B: M.165, E.168, N.169 Chain C: P.123 No protein-ligand interaction detected (PLIP) NAG.9: 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.10: 3 residues within 4Å: Chain B: M.287, N.289, S.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.291 NAG.15: 4 residues within 4Å: Chain A: P.123 Chain C: M.165, E.168, N.169 No protein-ligand interaction detected (PLIP) NAG.16: 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.17: 3 residues within 4Å: Chain C: M.287, N.289, S.291 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.291

3 x 6AT: 2-(methylsulfanyl)adenosine 5'-(tetrahydrogen triphosphate)(Non-covalent)

6AT.4: 18 residues within 4Å: Chain A: L.126, P.127, 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: NA.5, TRS.6, EDO.7 16 PLIP interactions: 8 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:K.62, C:T.171, C:F.173, A:N.278, 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:E.110, A:E.110, A:R.280 6AT.11: 18 residues within 4Å: Chain A: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain B: L.126, P.127, V.273, S.274, N.278, R.280, K.298 Ligands: NA.12, TRS.13, EDO.14 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:N.278, B:N.278, A:K.62, A:T.171, A:F.173 Water bridges: B:E.110, B:E.110, B:R.280 Salt bridges: B:R.280, B:K.298, B:K.298, A:K.62, A:K.62, A:K.62, A:K.64 pi-Cation interactions: A:K.64 6AT.18: 18 residues within 4Å: Chain B: K.62, V.63, K.64, T.171, I.172, F.173, M.199, I.214 Chain C: L.126, P.127, V.273, S.274, N.278, R.280, K.298 Ligands: NA.19, TRS.20, EDO.21 16 PLIP interactions: 8 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:K.62, B:T.171, B:F.173, C:N.278, 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:E.110, C:E.110, C:R.280

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

NA.5: 2 residues within 4Å: Chain A: E.110 Ligands: 6AT.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.110 NA.12: 2 residues within 4Å: Chain B: E.110 Ligands: 6AT.11 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.110 NA.19: 2 residues within 4Å: Chain C: E.110 Ligands: 6AT.18 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.6: 4 residues within 4Å: Chain A: L.126, P.127 Chain C: M.199 Ligands: 6AT.4 No protein-ligand interaction detected (PLIP) TRS.13: 4 residues within 4Å: Chain A: M.199 Chain B: L.126, P.127 Ligands: 6AT.11 No protein-ligand interaction detected (PLIP) TRS.20: 4 residues within 4Å: Chain B: M.199 Chain C: L.126, P.127 Ligands: 6AT.18 No protein-ligand interaction detected (PLIP)

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

EDO.7: 11 residues within 4Å: Chain A: S.274, G.276, Y.277, N.278, F.279 Chain C: V.60, T.61, K.62, F.173, K.175 Ligands: 6AT.4 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:N.278, A:N.278, C:K.62, C:K.62 EDO.14: 11 residues within 4Å: Chain A: V.60, T.61, K.62, F.173, K.175 Chain B: S.274, G.276, Y.277, N.278, F.279 Ligands: 6AT.11 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.278, B:N.278, A:K.62, A:K.62 EDO.21: 11 residues within 4Å: Chain B: V.60, T.61, K.62, F.173, K.175 Chain C: S.274, G.276, Y.277, N.278, F.279 Ligands: 6AT.18 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.278, C:N.278, B:K.62, B:K.62

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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