SMTL ID : 8zt2.1

Structure of calcium preference ATP-gated channel Apo-P2X1 in the Desensitized state 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

ATP.1: 15 residues within 4Å: Chain A: K.69, L.70, K.71, T.187, L.188, F.189, K.191, M.215 Chain B: K.141, D.171, S.287, N.291, R.293, K.310 Ligands: MG.7 20 PLIP interactions: 8 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:K.141, B:K.141, B:N.291, A:K.71, A:K.71, A:T.187, A:T.187, A:F.189 Water bridges: B:R.140 Salt bridges: B:K.141, B:R.293, B:K.310, B:K.310, A:K.69, A:K.69, A:K.69, A:K.71, A:K.71, A:K.191 pi-Cation interactions: A:K.71 ATP.8: 15 residues within 4Å: Chain B: K.69, L.70, K.71, T.187, L.188, F.189, K.191, M.215 Chain C: K.141, D.171, S.287, N.291, R.293, K.310 Ligands: MG.12 19 PLIP interactions: 11 interactions with chain B, 8 interactions with chain C Hydrogen bonds: B:K.71, B:T.187, B:T.187, B:F.189, C:K.141, C:K.141, C:N.291 Salt bridges: B:K.69, B:K.69, B:K.69, B:K.71, B:K.71, B:K.191, C:K.141, C:R.293, C:K.310, C:K.310 pi-Cation interactions: B:K.71 Water bridges: C:R.140 ATP.13: 17 residues within 4Å: Chain A: E.123, R.140, K.141, D.171, S.287, N.291, R.293, K.310 Chain C: K.69, L.70, K.71, T.187, F.189, K.191, M.215, V.230 Ligands: MG.5 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain A Hydrogen bonds: C:T.187, C:T.187, C:F.189, A:R.140, A:K.141, A:K.141, A:N.291 Salt bridges: C:K.69, C:K.69, C:K.69, C:K.71, C:K.191, A:K.141, A:R.293, A:K.310, A:K.310 pi-Cation interactions: C:K.71

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

NAG.2: 3 residues within 4Å: Chain A: E.209, N.211, Y.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.211 NAG.3: 5 residues within 4Å: Chain A: P.122, F.153, N.154, T.156, V.157 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.156 Hydrogen bonds: A:N.154, A:T.156, A:T.156 NAG.4: 5 residues within 4Å: Chain A: H.181, E.182, E.184, N.185 Chain B: E.139 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: E.209, N.211, Y.214 No protein-ligand interaction detected (PLIP) NAG.10: 4 residues within 4Å: Chain B: P.122, N.154, T.156, V.157 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:T.156 Hydrogen bonds: B:N.154, B:T.156, B:T.156 NAG.11: 5 residues within 4Å: Chain B: H.181, E.182, E.184, N.185 Chain C: E.139 No protein-ligand interaction detected (PLIP) NAG.14: 3 residues within 4Å: Chain C: E.209, N.211, Y.214 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain C: P.122, N.154, T.156, V.157 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.156 Hydrogen bonds: C:N.154, C:T.156, C:T.156 NAG.16: 5 residues within 4Å: Chain A: E.139 Chain C: H.181, E.182, E.184, N.185 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: E.123, D.171 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.171 MG.7: 3 residues within 4Å: Chain B: D.171, K.310 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.171 MG.12: 3 residues within 4Å: Chain C: D.171, K.310 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.171

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: F.298, V.299 Chain B: F.298, V.299 Chain C: F.298, V.299 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., Structural basis of ion permeation, calcium selectivity, and pore blocking at the P2X1 receptor. To Be Published

Release Date

2025-06-11

Peptides

P2X purinoceptor 1: 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 1

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