SMTL ID : 5svq.1

Crystal structure of the ATP-gated human P2X3 ion channel bound to competitive antagonist TNP-ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 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.166, N.169, R.216 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.165 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: 4 residues within 4Å: Chain A: M.102, M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.291, A:S.291 NAG.7: 4 residues within 4Å: Chain B: M.165, E.166, N.169, R.216 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:M.165 Hydrogen bonds: B:N.169 NAG.8: 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.9: 4 residues within 4Å: Chain B: M.102, M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.291, B:S.291 NAG.13: 4 residues within 4Å: Chain C: M.165, E.166, N.169, R.216 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:M.165 Hydrogen bonds: C:N.169 NAG.14: 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.15: 4 residues within 4Å: Chain C: M.102, M.287, N.289, S.291 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.291, C:S.291

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

NA.4: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.10, NA.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.322 NA.10: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.4, NA.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322 NA.16: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.4, NA.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: E.155, D.157 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: E.155, D.157 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain C: E.155, D.157 No protein-ligand interaction detected (PLIP)

3 x 128: SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE(Non-covalent)

128.6: 12 residues within 4Å: Chain A: D.157, D.265, N.278, R.280, K.298 Chain B: V.60, K.62, K.64, T.171, F.173, K.175, I.214 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:F.173 Hydrogen bonds: B:K.64, B:F.173, A:D.157, A:N.278, A:N.278 Salt bridges: B:K.64, B:K.64, A:R.280, A:K.298, A:K.298 pi-Cation interactions: B:K.64 128.12: 12 residues within 4Å: Chain B: D.157, D.265, N.278, R.280, K.298 Chain C: V.60, K.62, K.64, T.171, F.173, K.175, I.214 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:F.173 Hydrogen bonds: C:K.64, C:F.173, B:D.157, B:N.278, B:N.278 Salt bridges: C:K.64, C:K.64, B:R.280, B:K.298, B:K.298 pi-Cation interactions: C:K.64 128.18: 12 residues within 4Å: Chain A: V.60, K.62, K.64, T.171, F.173, K.175, I.214 Chain C: D.157, D.265, N.278, R.280, K.298 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:D.157, C:N.278, C:N.278, A:K.64, A:F.173 Salt bridges: C:R.280, C:K.298, C:K.298, A:K.64, A:K.64 Hydrophobic interactions: A:F.173 pi-Cation interactions: A:K.64

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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