SMTL ID : 8jv5.1

Cryo-EM structure of the zebrafish P2X4 receptor in complex with BX430

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x P73: 1-[2,6-bis(bromanyl)-4-propan-2-yl-phenyl]-3-pyridin-3-yl-urea(Non-covalent)

P73.1: 13 residues within 4Å: Chain A: R.77, W.79, A.82, D.83, I.85, I.86, L.97, I.102, F.291, K.293, I.307 Chain B: Y.294, E.302 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.102 Hydrogen bonds: A:D.83, A:D.83, A:K.293 pi-Stacking: A:W.79 pi-Cation interactions: A:K.293 P73.5: 13 residues within 4Å: Chain B: R.77, W.79, A.82, D.83, I.85, I.86, L.97, I.102, F.291, K.293, I.307 Chain C: Y.294, E.302 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:I.102 Hydrogen bonds: B:D.83, B:D.83, B:K.293 pi-Stacking: B:W.79 pi-Cation interactions: B:K.293 P73.9: 12 residues within 4Å: Chain A: Y.294, E.302 Chain C: R.77, W.79, A.82, D.83, I.86, L.97, I.102, F.291, K.293, I.307 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:I.102 Hydrogen bonds: C:D.83, C:D.83, C:K.293 pi-Stacking: C:W.79 pi-Cation interactions: C:K.293

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

NAG.2: 1 residues within 4Å: Chain A: N.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.205 NAG.3: 3 residues within 4Å: Chain A: A.175, D.176, N.179 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.175 NAG.4: 3 residues within 4Å: Chain A: N.70, E.76 Chain B: R.129 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.70, A:E.76, B:R.129 NAG.6: 1 residues within 4Å: Chain B: N.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.205 NAG.7: 3 residues within 4Å: Chain B: A.175, D.176, N.179 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.175 NAG.8: 3 residues within 4Å: Chain B: N.70, E.76 Chain C: R.129 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.70, B:E.76, C:R.129 NAG.10: 1 residues within 4Å: Chain C: N.205 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.205 NAG.11: 3 residues within 4Å: Chain C: A.175, D.176, N.179 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.175 NAG.12: 3 residues within 4Å: Chain A: R.129 Chain C: N.70, E.76 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.129, C:N.70, C:E.76

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, M. et al., Structural insights into the allosteric inhibition of P2X4 receptors. Nat Commun (2023)

Release Date

2023-10-18

Peptides

P2X purinoceptor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor