SMTL ID : 9c2a.1

Cryo-EM structure of the human P2X1 receptor in the apo closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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.1: 4 residues within 4Å: Chain A: P.121, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.121 NAG-NAG.2: 4 residues within 4Å: Chain B: P.121, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.121 NAG-NAG.3: 4 residues within 4Å: Chain C: P.121, N.153, T.155, V.156 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.121

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

NAG.4: 1 residues within 4Å: Chain A: N.242 No protein-ligand interaction detected (PLIP) NAG.5: 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.6: 1 residues within 4Å: Chain A: N.300 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain B: N.242 No protein-ligand interaction detected (PLIP) NAG.10: 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.11: 1 residues within 4Å: Chain B: N.300 No protein-ligand interaction detected (PLIP) NAG.14: 1 residues within 4Å: Chain C: N.242 No protein-ligand interaction detected (PLIP) NAG.15: 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.16: 1 residues within 4Å: Chain C: N.300 No protein-ligand interaction detected (PLIP)

6 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.7: 5 residues within 4Å: Chain A: I.45, L.50, W.265, H.269 Ligands: Y01.8 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.45, A:I.45, A:L.50, A:L.50, A:W.265 Hydrogen bonds: A:H.266 Salt bridges: A:H.266, A:H.269 Y01.8: 10 residues within 4Å: Chain A: V.44, I.45, F.49, L.50, Y.55, D.264, F.326, T.331, I.335 Ligands: Y01.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.44, A:I.45, A:F.49, A:F.49, A:F.49, A:L.50, A:Y.55, A:Y.55, A:Y.55, A:F.326, A:I.335, A:I.335, A:I.335 Y01.12: 5 residues within 4Å: Chain B: I.45, L.50, W.265, H.269 Ligands: Y01.13 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.45, B:I.45, B:L.50, B:L.50, B:W.265 Hydrogen bonds: B:H.266 Salt bridges: B:H.266, B:H.269 Y01.13: 10 residues within 4Å: Chain B: V.44, I.45, F.49, L.50, Y.55, D.264, F.326, T.331, I.335 Ligands: Y01.12 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.44, B:I.45, B:F.49, B:F.49, B:F.49, B:L.50, B:Y.55, B:Y.55, B:Y.55, B:F.326, B:I.335, B:I.335, B:I.335 Y01.17: 5 residues within 4Å: Chain C: I.45, L.50, W.265, H.269 Ligands: Y01.18 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.45, C:I.45, C:L.50, C:L.50, C:W.265 Hydrogen bonds: C:H.266 Salt bridges: C:H.266, C:H.269 Y01.18: 10 residues within 4Å: Chain C: V.44, I.45, F.49, L.50, Y.55, D.264, F.326, T.331, I.335 Ligands: Y01.17 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:V.44, C:I.45, C:F.49, C:F.49, C:F.49, C:L.50, C:Y.55, C:Y.55, C:Y.55, C:F.326, C:I.335, C:I.335, C:I.335

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.
Show / Hide

P2X purinoceptor 1

Related Entries With Identical Sequence