SMTL ID : 9lxc.1

Cryo-EM structure of the P2X1 receptor bound to NF449

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 3 residues within 4Å: Chain A: F.21, Y.27, D.236 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.21, A:Y.27, A:D.236 CLR.3: 3 residues within 4Å: Chain B: Y.27, D.236, W.237 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.27 CLR.5: 3 residues within 4Å: Chain C: D.236, W.237, F.298 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.236, C:W.237, C:F.298

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

01.2: 23 residues within 4Å: Chain A: K.40, L.41, K.42, G.43, L.44, V.59, N.156, F.157, T.158, F.160, R.175, L.177, E.179, V.181, M.186, K.187, T.188, L.190 Chain B: K.108, R.111, K.112, N.256, R.264 25 PLIP interactions: 19 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:K.42, A:K.42, A:T.158, A:F.160, A:L.177, A:L.177, A:M.186, A:K.187, A:L.190, A:L.190 Hydrogen bonds: A:L.41, A:L.44, A:T.158, A:R.175, A:V.178, A:V.181, A:K.187, B:R.111, B:R.111, B:R.111 Salt bridges: A:K.40, A:K.42, B:K.108, B:R.111, B:R.264 01.4: 27 residues within 4Å: Chain B: K.40, L.41, K.42, G.43, L.44, N.156, F.157, T.158, F.160, L.177, V.178, E.179, E.180, V.181, A.183, K.187, T.188, C.189, L.190, L.198, P.200, V.201 Chain C: K.108, R.111, A.113, N.262, R.264 28 PLIP interactions: 22 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:K.40, B:K.42, B:K.187, B:V.201 Hydrogen bonds: B:L.44, B:E.153, B:T.158, B:T.158, B:V.178, B:E.179, B:V.181, B:N.182, B:A.183, B:T.188, B:T.188, B:L.198, B:L.198, C:R.111, C:R.111, C:N.256, C:R.264 Salt bridges: B:K.40, B:K.42, B:K.187, C:K.108, C:R.111 pi-Stacking: B:F.160 pi-Cation interactions: B:K.187 01.6: 29 residues within 4Å: Chain A: K.108, R.111, A.113, N.262, R.264 Chain C: K.40, L.41, K.42, G.43, L.44, N.156, F.157, T.158, F.160, L.177, V.178, E.179, E.180, V.181, N.182, H.185, M.186, K.187, T.188, C.189, L.190, C.199, F.202, Q.203 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:K.40, C:K.42, C:F.160, C:F.160, C:L.177, C:L.190, C:F.202 Hydrogen bonds: C:K.42, C:L.44, C:T.158, C:T.158, C:V.181, C:N.182, C:K.187, C:K.187, C:K.187, C:T.188, C:C.189, A:R.111 Salt bridges: C:K.40, C:K.42, C:H.185, A:K.108, A:R.111, A:R.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qiang, Y.T. et al., Structural basis of the multiple ligand binding mechanisms of the P2X1 receptor. Acta Pharmacol.Sin. (2025)

Release Date

2025-04-16

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