SMTL ID : 9ddx.1

Cryo-EM structure of the human P2X2 receptor in conformation II of the ATP-bound desensitized state

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: P.151, N.152, G.200 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.151 Water bridges: A:P.151 NAG.2: 3 residues within 4Å: Chain A: H.90, N.91, D.99 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.90 NAG.5: 3 residues within 4Å: Chain B: P.151, N.152, G.200 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.151 Water bridges: B:P.151 NAG.6: 3 residues within 4Å: Chain B: H.90, N.91, D.99 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.90 NAG.8: 3 residues within 4Å: Chain C: P.151, N.152, G.200 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.151 Water bridges: C:P.151 NAG.9: 3 residues within 4Å: Chain C: H.90, N.91, D.99 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.90

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 16 residues within 4Å: Chain A: K.39, V.40, K.41, T.154, I.155, L.156, K.158, L.181, K.182, I.196 Chain C: R.88, L.108, A.253, N.258, R.260, K.277 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:K.41, A:T.154, A:T.154, A:L.156, A:K.182, C:N.258 Water bridges: A:K.158 Salt bridges: A:K.39, A:K.39, A:K.39, A:K.41, A:K.158, C:R.260, C:K.277, C:K.277 pi-Cation interactions: A:K.41 ATP.4: 16 residues within 4Å: Chain A: R.88, L.108, A.253, N.258, R.260, K.277 Chain B: K.39, V.40, K.41, T.154, I.155, L.156, K.158, L.181, K.182, I.196 16 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:K.41, B:T.154, B:T.154, B:L.156, B:K.182, A:N.258 Water bridges: B:K.158 Salt bridges: B:K.39, B:K.39, B:K.39, B:K.41, B:K.158, A:R.260, A:K.277, A:K.277 pi-Cation interactions: B:K.41 ATP.7: 16 residues within 4Å: Chain B: R.88, L.108, A.253, N.258, R.260, K.277 Chain C: K.39, V.40, K.41, T.154, I.155, L.156, K.158, L.181, K.182, I.196 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:K.41, C:T.154, C:T.154, C:L.156, C:K.182, B:N.258 Water bridges: C:K.158 Salt bridges: C:K.39, C:K.39, C:K.39, C:K.41, C:K.158, B:R.260, B:K.277, B:K.277 pi-Cation interactions: C:K.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Westermann, F.G. et al., Subtype-specific structural features of the hearing loss-associated human P2X2 receptor. Proc.Natl.Acad.Sci.USA (2025)

Release Date

2025-09-24

Peptides

P2X purinoceptor 2: 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 2