SMTL ID : 9c2c.1

Cryo-EM structure of the human P2X1 receptor in the NF449-bound inhibited state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.242, T.245 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.245 NAG.2: 5 residues within 4Å: Chain A: R.180, E.181, E.183, N.184 Ligands: 01.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.183 NAG.5: 4 residues within 4Å: Chain A: P.121, I.125, N.153, V.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.153 NAG.6: 2 residues within 4Å: Chain B: N.242, T.245 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.245 NAG.7: 5 residues within 4Å: Chain B: R.180, E.181, E.183, N.184 Ligands: 01.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.183 NAG.10: 4 residues within 4Å: Chain B: P.121, I.125, N.153, V.156 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.153 NAG.11: 2 residues within 4Å: Chain C: N.242, T.245 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.245 NAG.12: 5 residues within 4Å: Chain C: R.180, E.181, E.183, N.184 Ligands: 01.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.183 NAG.15: 4 residues within 4Å: Chain C: P.121, I.125, N.153, V.156 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.153

6 x 01: 4,4',4'',4'''-{carbonylbis[azanediylbenzene-5,1,3-triylbis(carbonylazanediyl)]}tetra(benzene-1,3-disulfonic acid)

01.3: 21 residues within 4Å: Chain A: K.68, L.69, K.70, V.87, N.184, T.186, F.188, L.205, T.216, C.217, L.218, H.220, H.224, P.228, V.229, Q.231 Chain C: K.136, K.138, R.292 Ligands: NAG.2, 01.4 22 PLIP interactions: 20 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:K.68, A:K.68, A:N.184, A:T.186, A:T.216, A:L.218, A:L.218, A:V.229 Hydrogen bonds: A:L.69, A:N.184, A:C.217, A:C.217, A:C.217, A:L.218, A:Q.231, A:Q.231 Salt bridges: A:K.68, A:H.220, A:H.224, C:K.136, C:K.138 pi-Stacking: A:F.188 01.4: 13 residues within 4Å: Chain A: K.70, K.215, T.216, C.217, H.224, L.226, C.227 Chain C: K.138, R.139, K.140, R.292, K.309 Ligands: 01.3 15 PLIP interactions: 7 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:K.215, C:K.138 Hydrogen bonds: A:T.216, A:T.216, A:T.216, A:L.226, A:L.226 Salt bridges: A:H.224, C:K.138, C:R.139, C:R.139, C:K.140, C:R.292, C:K.309 pi-Cation interactions: C:R.139 01.8: 21 residues within 4Å: Chain A: K.136, K.138, R.292 Chain B: K.68, L.69, K.70, V.87, N.184, T.186, F.188, L.205, T.216, C.217, L.218, H.220, H.224, P.228, V.229, Q.231 Ligands: NAG.7, 01.9 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:K.68, B:K.68, B:N.184, B:T.186, B:T.216, B:L.218, B:L.218, B:V.229 Hydrogen bonds: B:L.69, B:N.184, B:C.217, B:C.217, B:C.217, B:L.218, B:Q.231, B:Q.231 Salt bridges: B:K.68, B:H.220, B:H.224, A:K.136, A:K.138 pi-Stacking: B:F.188 01.9: 13 residues within 4Å: Chain A: K.138, R.139, K.140, R.292, K.309 Chain B: K.70, K.215, T.216, C.217, H.224, L.226, C.227 Ligands: 01.8 15 PLIP interactions: 8 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:K.138, B:K.215 Salt bridges: A:K.138, A:R.139, A:R.139, A:K.140, A:R.292, A:K.309, B:H.224 pi-Cation interactions: A:R.139 Hydrogen bonds: B:T.216, B:T.216, B:T.216, B:L.226, B:L.226 01.13: 21 residues within 4Å: Chain B: K.136, K.138, R.292 Chain C: K.68, L.69, K.70, V.87, N.184, T.186, F.188, L.205, T.216, C.217, L.218, H.220, H.224, P.228, V.229, Q.231 Ligands: NAG.12, 01.14 22 PLIP interactions: 20 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:K.68, C:K.68, C:N.184, C:T.186, C:T.216, C:L.218, C:L.218, C:V.229 Hydrogen bonds: C:L.69, C:N.184, C:C.217, C:C.217, C:C.217, C:L.218, C:Q.231, C:Q.231 Salt bridges: C:K.68, C:H.220, C:H.224, B:K.136, B:K.138 pi-Stacking: C:F.188 01.14: 13 residues within 4Å: Chain B: K.138, R.139, K.140, R.292, K.309 Chain C: K.70, K.215, T.216, C.217, H.224, L.226, C.227 Ligands: 01.13 15 PLIP interactions: 7 interactions with chain C, 8 interactions with chain B Hydrophobic interactions: C:K.215, B:K.138 Hydrogen bonds: C:T.216, C:T.216, C:T.216, C:L.226, C:L.226 Salt bridges: C:H.224, B:K.138, B:R.139, B:R.139, B:K.140, B:R.292, B:K.309 pi-Cation interactions: B:R.139

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
C

C
B

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor 1

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