SMTL ID : 5svt.1

Anomalous Cs+ signal reveals the site of Na+ ion entry to the channel pore of the human P2X3 ion channel through the extracellular fenestrations

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.79 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 C: P.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 NAG.2: 3 residues within 4Å: Chain A: N.193, W.252, D.253 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.252 Hydrogen bonds: A:N.193 NAG.3: 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.6: 4 residues within 4Å: Chain A: P.127 Chain B: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.169 NAG.7: 3 residues within 4Å: Chain B: N.193, W.252, D.253 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.252 Hydrogen bonds: B:N.193 NAG.8: 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.11: 4 residues within 4Å: Chain B: P.127 Chain C: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.169 NAG.12: 3 residues within 4Å: Chain C: N.193, W.252, D.253 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.252 Hydrogen bonds: C:N.193 NAG.13: 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 MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: E.108, E.155, D.157 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: E.108, E.155, D.157 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: E.108, E.155, D.157 No protein-ligand interaction detected (PLIP)

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

NA.5: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.10, NA.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322 NA.10: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.5, NA.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322 NA.15: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.5, NA.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322

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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