SMTL ID : 8ztd.1

Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 5 in the presence of 10 mM Calcium ion

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.68, L.69, K.70, T.186, F.188, K.190, M.214 Chain B: R.139, K.140, D.170, S.286, N.290, R.292, K.309 Ligands: MG.8 19 PLIP interactions: 7 interactions with chain B, 12 interactions with chain A Hydrogen bonds: B:R.139, B:D.170, B:N.290, A:K.70, A:K.70, A:T.186, A:T.186, A:F.188 Salt bridges: B:K.140, B:R.292, B:K.309, B:K.309, A:K.68, A:K.68, A:K.68, A:K.70, A:K.70, A:K.190 pi-Cation interactions: A:K.70 ATP.5: 15 residues within 4Å: Chain A: R.139, K.140, D.170, S.286, N.290, R.292, K.309 Chain C: K.68, L.69, K.70, T.186, F.188, K.190, M.214 Ligands: MG.6 19 PLIP interactions: 7 interactions with chain A, 12 interactions with chain C Hydrogen bonds: A:R.139, A:K.140, A:D.170, A:N.290, C:K.70, C:K.70, C:T.186, C:T.186, C:F.188 Salt bridges: A:R.292, A:K.309, A:K.309, C:K.68, C:K.68, C:K.68, C:K.70, C:K.70, C:K.190 pi-Cation interactions: C:K.70 ATP.13: 14 residues within 4Å: Chain B: K.68, L.69, K.70, T.186, F.188, M.214 Chain C: R.139, K.140, D.170, S.286, N.290, R.292, K.309 Ligands: MG.14 17 PLIP interactions: 8 interactions with chain B, 9 interactions with chain C Hydrogen bonds: B:T.186, B:T.186, B:F.188, C:R.139, C:K.140, C:D.170, C:D.170, C:D.170, C:N.290 Salt bridges: B:K.68, B:K.68, B:K.70, C:R.292, C:K.309, C:K.309 pi-Cation interactions: B:K.70, B:K.70

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

NAG.2: 4 residues within 4Å: Chain A: E.208, N.210, T.212, Y.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.210, A:T.212, A:T.212 NAG.3: 4 residues within 4Å: Chain A: P.121, N.153, T.155, V.156 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.155 Hydrogen bonds: A:N.153, A:T.155 NAG.4: 5 residues within 4Å: Chain A: H.180, E.181, E.183, N.184 Chain B: E.138 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain B: E.208, N.210, Y.213 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.212, B:T.212 NAG.10: 4 residues within 4Å: Chain B: P.121, N.153, T.155, V.156 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.155 Hydrogen bonds: B:N.153, B:T.155 NAG.11: 5 residues within 4Å: Chain B: H.180, E.181, E.183, N.184 Chain C: E.138 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain C: E.208, N.210, Y.213 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain C: P.121, N.153, T.155, V.156 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.155 Hydrogen bonds: C:N.153, C:T.155 NAG.17: 5 residues within 4Å: Chain A: E.138 Chain C: H.180, E.181, E.183, N.184 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.122, D.170 Ligands: ATP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.122, A:D.170 MG.8: 2 residues within 4Å: Chain B: D.170 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.170 MG.14: 2 residues within 4Å: Chain C: D.170 Ligands: ATP.13 No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 2 residues within 4Å: Chain A: D.97 Chain C: D.97 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.97 CA.12: 6 residues within 4Å: Chain A: F.297, V.298 Chain B: F.297, V.298 Chain C: F.297, V.298 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.
Show / Hide

P2X purinoceptor 1

Related Entries With Identical Sequence