SMTL ID : 9b73.1

Cryo-EM structure of the desensitised ATP-bound human P2X1 receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

ATP.1: 17 residues within 4Å: Chain A: K.68, L.69, K.70, T.186, L.187, F.188, K.190, M.214, V.229 Chain C: R.139, K.140, D.170, S.286, N.290, R.292, K.309 Ligands: MG.11 19 PLIP interactions: 9 interactions with chain A, 10 interactions with chain C Hydrogen bonds: A:K.70, A:T.186, A:F.188, C:K.140, C:N.290 Salt bridges: A:K.68, A:K.68, A:K.68, A:K.70, A:K.190, C:R.292, C:K.309, C:K.309 pi-Cation interactions: A:K.70 Water bridges: C:E.122, C:E.122, C:R.139, C:K.309, C:K.309 ATP.6: 17 residues within 4Å: Chain A: R.139, K.140, D.170, S.286, N.290, R.292, K.309 Chain B: K.68, L.69, K.70, T.186, L.187, F.188, K.190, M.214, V.229 Ligands: MG.5 20 PLIP interactions: 10 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:K.70, B:T.186, B:T.186, B:F.188, A:K.140, A:N.290 Salt bridges: B:K.68, B:K.68, B:K.68, B:K.70, B:K.190, A:R.292, A:K.309, A:K.309 pi-Cation interactions: B:K.70 Water bridges: A:E.122, A:E.122, A:E.122, A:R.139, A:D.170 ATP.12: 17 residues within 4Å: Chain B: R.139, K.140, D.170, S.286, N.290, R.292, K.309 Chain C: K.68, L.69, K.70, T.186, L.187, F.188, K.190, M.214, V.229 Ligands: MG.10 22 PLIP interactions: 10 interactions with chain C, 12 interactions with chain B Hydrogen bonds: C:K.70, C:T.186, C:T.186, C:F.188, B:K.140, B:N.290 Salt bridges: C:K.68, C:K.68, C:K.68, C:K.70, C:K.190, B:R.292, B:K.309, B:K.309 pi-Cation interactions: C:K.70 Water bridges: B:E.122, B:E.122, B:E.122, B:E.122, B:R.139, B:K.309, B:K.309

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

NAG.2: 6 residues within 4Å: Chain A: P.121, F.152, N.153, T.155, V.156, D.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.153, A:D.171 NAG.3: 4 residues within 4Å: Chain A: R.180, E.181, E.183, N.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.183 NAG.4: 2 residues within 4Å: Chain A: N.242, S.244 No protein-ligand interaction detected (PLIP) NAG.7: 6 residues within 4Å: Chain B: P.121, F.152, N.153, T.155, V.156, D.171 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.153, B:D.171 NAG.8: 4 residues within 4Å: Chain B: R.180, E.181, E.183, N.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.183 NAG.9: 2 residues within 4Å: Chain B: N.242, S.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.245 NAG.13: 6 residues within 4Å: Chain C: P.121, F.152, N.153, T.155, V.156, D.171 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.153, C:D.171 NAG.14: 4 residues within 4Å: Chain C: R.180, E.181, E.183, N.184 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.183 NAG.15: 2 residues within 4Å: Chain C: N.242, S.244 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.245

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: D.170, R.292, K.309 Ligands: ATP.6 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.170, A:D.170, H2O.1, H2O.1, H2O.2 MG.10: 4 residues within 4Å: Chain B: D.170, R.292, K.309 Ligands: ATP.12 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.170, B:D.170, H2O.2, H2O.2, H2O.2 MG.11: 4 residues within 4Å: Chain C: D.170, R.292, K.309 Ligands: ATP.1 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.170, C:D.170, H2O.1, H2O.1, H2O.2

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bennetts, F.M. et al., Structural insights into the human P2X1 receptor and ligand interactions. Nat Commun (2024)

Release Date

2024-10-09

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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