SMTL ID : 9ddw.1

Cryo-EM structure of the human P2X2 receptor in conformation I 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.193, N.194, G.242 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.193 NAG.2: 3 residues within 4Å: Chain A: H.132, N.133, D.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.132 NAG.5: 3 residues within 4Å: Chain B: P.193, N.194, G.242 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.193 NAG.6: 3 residues within 4Å: Chain B: H.132, N.133, D.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.132 NAG.8: 3 residues within 4Å: Chain C: P.193, N.194, G.242 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.193 NAG.9: 3 residues within 4Å: Chain C: H.132, N.133, D.141 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.132

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

ATP.3: 17 residues within 4Å: Chain A: K.81, V.82, K.83, T.196, I.197, L.198, K.200, L.223, K.224, I.238 Chain C: R.130, A.295, S.296, S.297, N.300, R.302, K.319 21 PLIP interactions: 14 interactions with chain A, 7 interactions with chain C Hydrogen bonds: A:T.196, A:T.196, A:L.198, A:K.224, C:S.296, C:N.300 Water bridges: A:K.83, A:K.200, A:K.200, A:K.200, C:S.296, C:S.297 Salt bridges: A:K.81, A:K.81, A:K.81, A:K.83, A:K.200, C:R.302, C:K.319, C:K.319 pi-Cation interactions: A:K.83 ATP.4: 17 residues within 4Å: Chain A: R.130, A.295, S.296, S.297, N.300, R.302, K.319 Chain B: K.81, V.82, K.83, T.196, I.197, L.198, K.200, L.223, K.224, I.238 17 PLIP interactions: 9 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:T.196, B:T.196, B:L.198, B:K.224, A:S.296, A:N.300 Salt bridges: B:K.81, B:K.81, B:K.81, B:K.83, A:R.302, A:K.319, A:K.319 pi-Cation interactions: B:K.83 Water bridges: A:S.296, A:S.297, A:S.297 ATP.7: 17 residues within 4Å: Chain B: R.130, A.295, S.296, S.297, N.300, R.302, K.319 Chain C: K.81, V.82, K.83, T.196, I.197, L.198, K.200, L.223, K.224, I.238 18 PLIP interactions: 10 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:T.196, C:T.196, C:L.198, C:K.224, B:S.296, B:N.300 Salt bridges: C:K.81, C:K.81, C:K.81, C:K.83, C:K.200, B:R.302, B:K.319, B:K.319 pi-Cation interactions: C:K.83 Water bridges: B:S.296, B:S.297, B:S.297

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

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