SMTL ID : 9c2b.1

Cryo-EM structure of the human P2X1 receptor in the ATP-bound desensitized state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: P.121, I.125, F.152, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.125 NAG-NAG-BMA.3: 6 residues within 4Å: Chain B: P.121, I.125, F.152, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.125 NAG-NAG-BMA.5: 6 residues within 4Å: Chain C: P.121, I.125, F.152, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.125

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 4 residues within 4Å: Chain A: R.180, E.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: R.180, E.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: R.180, E.181, E.183, N.184 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: D.170, R.292, K.309 Ligands: ATP.13 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.170, A:D.170 MG.10: 4 residues within 4Å: Chain B: D.170, R.292, K.309 Ligands: ATP.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.170, B:D.170 MG.14: 4 residues within 4Å: Chain C: D.170, R.292, K.309 Ligands: ATP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.170, C:D.170

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

NAG.8: 1 residues within 4Å: Chain A: N.242 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain B: N.242 No protein-ligand interaction detected (PLIP) NAG.15: 1 residues within 4Å: Chain C: N.242 No protein-ligand interaction detected (PLIP)

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

ATP.9: 15 residues within 4Å: Chain A: K.68, L.69, K.70, T.186, L.187, F.188, M.214, V.229 Chain B: K.140, D.170, S.286, N.290, R.292, K.309 Ligands: MG.10 16 PLIP interactions: 6 interactions with chain B, 10 interactions with chain A Hydrogen bonds: B:N.290, A:T.186, A:T.186, A:F.188 Water bridges: B:E.122, B:K.140, A:K.70 Salt bridges: B:R.292, B:K.309, B:K.309, A:K.68, A:K.68, A:K.68, A:K.70, A:K.190 pi-Cation interactions: A:K.70 ATP.12: 15 residues within 4Å: Chain B: K.68, L.69, K.70, T.186, L.187, F.188, M.214, V.229 Chain C: K.140, D.170, S.286, N.290, R.292, K.309 Ligands: MG.14 16 PLIP interactions: 10 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:T.186, B:T.186, B:F.188, C:N.290 Water bridges: B:K.70, C:E.122, C:K.140 Salt bridges: B:K.68, B:K.68, B:K.68, B:K.70, B:K.190, C:R.292, C:K.309, C:K.309 pi-Cation interactions: B:K.70 ATP.13: 15 residues within 4Å: Chain A: 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, M.214, V.229 Ligands: MG.7 16 PLIP interactions: 10 interactions with chain C, 6 interactions with chain A Hydrogen bonds: C:T.186, C:T.186, C:F.188, A:N.290 Water bridges: C:K.70, A:E.122, A:K.140 Salt bridges: C:K.68, C:K.68, C:K.68, C:K.70, C:K.190, A:R.292, A:K.309, A:K.309 pi-Cation interactions: C:K.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oken, A.C. et al., Cryo-EM structures of the human P2X1 receptor reveal subtype-specific architecture and antagonism by supramolecular ligand-binding. 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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