SMTL ID : 5svs.1

Anomalous Mn2+ signal reveals a divalent cation-binding site in the head domain of the ATP-gated human P2X3 ion channel

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.03 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.291, A:S.291 NAG.8: 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.9: 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.10: 3 residues within 4Å: Chain B: M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.291, B:S.291 NAG.15: 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.16: 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.17: 3 residues within 4Å: Chain C: M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: 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.11: 3 residues within 4Å: Chain B: E.108, E.155, D.157 No protein-ligand interaction detected (PLIP) MG.18: 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.12, NA.19 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.322 NA.12: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.5, NA.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.322 NA.19: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.5, NA.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.322

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.6: 12 residues within 4Å: Chain A: Y.284, E.292 Chain B: R.72, M.74, S.77, D.78, T.81, M.95, F.279, F.281, K.283, L.297 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.292, B:K.283 PG4.13: 12 residues within 4Å: Chain B: Y.284, E.292 Chain C: R.72, M.74, S.77, D.78, T.81, M.95, F.279, F.281, K.283, L.297 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.292, C:K.283 PG4.20: 12 residues within 4Å: Chain A: R.72, M.74, S.77, D.78, T.81, M.95, F.279, F.281, K.283, L.297 Chain C: Y.284, E.292 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.283, C:E.292

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

EDO.7: 2 residues within 4Å: Chain A: N.100, M.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.100 EDO.14: 2 residues within 4Å: Chain B: N.100, M.287 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100 EDO.21: 2 residues within 4Å: Chain C: N.100, M.287 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.100

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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