SMTL ID : 8jv6.1

Cryo-EM structure of the zebrafish P2X4 receptor in complex with BAY-1797

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

12 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.1: 1 residues within 4Å: Chain A: N.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.205 NAG.2: 1 residues within 4Å: Chain A: N.105 No protein-ligand interaction detected (PLIP) NAG.3: 3 residues within 4Å: Chain A: A.175, E.178, N.179 No protein-ligand interaction detected (PLIP) NAG.5: 2 residues within 4Å: Chain A: N.70 Chain B: R.129 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.129, A:N.70 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: 2 residues within 4Å: Chain B: N.105, T.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.105, B:T.107 NAG.8: 3 residues within 4Å: Chain B: N.70, E.76 Chain C: R.129 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.129, B:N.70 NAG.9: 3 residues within 4Å: Chain B: A.175, E.178, N.179 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain C: N.205, Y.208 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.205 NAG.12: 1 residues within 4Å: Chain C: N.105 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain A: R.129 Chain C: N.70 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.70, A:R.129 NAG.14: 3 residues within 4Å: Chain C: A.175, E.178, N.179 No protein-ligand interaction detected (PLIP)

3 x P6E: N-[4-(3-chloranylphenoxy)-3-sulfamoyl-phenyl]-2-phenyl-ethanamide(Non-covalent)

P6E.4: 18 residues within 4Å: Chain A: R.77, W.79, A.82, D.83, I.85, I.86, P.88, M.100, I.102, F.291, K.293, I.307 Chain B: A.292, Y.294, E.302 Chain C: P.88 Ligands: P6E.10, P6E.15 11 PLIP interactions: 1 interactions with chain C, 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:P.88, A:W.79, A:I.86, A:I.102, A:F.291, A:I.307 Hydrogen bonds: A:A.82, A:D.83, A:K.293, B:A.292 pi-Cation interactions: A:K.293 P6E.10: 18 residues within 4Å: Chain A: P.88 Chain B: R.77, W.79, A.82, D.83, I.85, I.86, P.88, M.100, I.102, F.291, K.293, I.307 Chain C: A.292, Y.294, E.302 Ligands: P6E.4, P6E.15 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:W.79, B:I.86, B:I.102, B:F.291, B:I.307 Hydrogen bonds: B:A.82, B:D.83, B:K.293, C:A.292 pi-Cation interactions: B:K.293 P6E.15: 19 residues within 4Å: Chain A: F.291, A.292, Y.294, E.302 Chain B: P.88 Chain C: R.77, W.79, A.82, D.83, I.85, I.86, P.88, M.100, I.102, F.291, K.293, I.307 Ligands: P6E.4, P6E.10 11 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: C:W.79, C:I.86, C:I.102, C:F.291, C:I.307, B:P.88 Hydrogen bonds: C:A.82, C:D.83, C:K.293, A:A.292 pi-Cation interactions: C:K.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, C. 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.
Show / Hide

P2X purinoceptor