SMTL ID : 8jv8.1

Cryo-EM structure of the panda P2X7 receptor in complex with PPNDS

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.163, E.166, N.167 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.167 NAG.2: 2 residues within 4Å: Chain A: N.193, T.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.195 NAG.4: 3 residues within 4Å: Chain B: N.163, E.166, N.167 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167 NAG.5: 2 residues within 4Å: Chain B: N.193, T.195 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.195 NAG.7: 3 residues within 4Å: Chain C: N.163, E.166, N.167 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain C: N.193, T.195 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.195

3 x 20V: 3-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]-7-nitronaphthalene-1,5-disulfonic acid(Non-covalent)

20V.3: 11 residues within 4Å: Chain A: Q.123, V.153, K.154, S.266, L.267, Y.268, R.274, K.291 Chain B: K.46, I.194, T.195 11 PLIP interactions: 1 interactions with chain B, 10 interactions with chain A Salt bridges: B:K.46, A:K.125, A:R.274, A:K.291 Hydrophobic interactions: A:V.153, A:Y.268 Hydrogen bonds: A:Q.123, A:K.154, A:S.266, A:Y.268, A:K.291 20V.6: 10 residues within 4Å: Chain B: Q.123, V.153, S.266, L.267, Y.268, R.274, K.291 Chain C: K.46, I.194, T.195 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.153, B:Y.268 Hydrogen bonds: B:Q.123, B:K.154, B:S.266, B:Y.268, B:K.291 Salt bridges: B:K.125, B:R.274, B:K.291, C:K.46 20V.9: 10 residues within 4Å: Chain A: K.46, I.194, T.195 Chain C: V.153, K.154, S.266, L.267, Y.268, R.274, K.291 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:V.153, C:Y.268 Hydrogen bonds: C:K.154, C:S.266, C:Y.268, C:K.291 Salt bridges: C:K.125, C:R.274, C:K.291, A:K.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sheng, D. et al., Structural insights into the orthosteric inhibition of P2X receptors by non-ATP analog antagonists. Elife (2024)

Release Date

2023-11-29

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

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