SMTL ID : 9b95.1

Cryo-EM structure of the closed NF449-bound human P2X1 receptor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

01.1: 28 residues within 4Å: Chain A: K.68, L.69, K.70, G.71, L.72, N.184, F.185, T.186, F.188, L.205, V.206, E.207, E.208, V.209, H.213, M.214, K.215, C.217, L.218, P.228, V.229 Chain C: K.136, R.139, K.140, A.141, N.290, R.292, K.309 37 PLIP interactions: 27 interactions with chain A, 10 interactions with chain C Hydrophobic interactions: A:K.68, A:K.70, A:T.186, A:V.209, A:K.215, A:L.218, A:L.218, A:P.228, A:V.229 Hydrogen bonds: A:L.72, A:T.186, A:V.206, A:E.207, A:E.208, A:E.208, A:V.209, A:K.215, A:C.217, A:C.217, C:A.137, C:R.139, C:R.139, C:K.140, C:N.290, C:N.290 Water bridges: A:K.68, A:G.71, A:G.71, C:R.292 Salt bridges: A:K.68, A:K.70, A:H.213, A:K.215, C:K.136, C:R.292 pi-Stacking: A:F.188 pi-Cation interactions: C:R.139 01.3: 28 residues within 4Å: Chain A: K.136, R.139, K.140, A.141, N.290, R.292, K.309 Chain B: K.68, L.69, K.70, G.71, L.72, N.184, F.185, T.186, F.188, L.205, V.206, E.207, E.208, V.209, H.213, M.214, K.215, C.217, L.218, P.228, V.229 37 PLIP interactions: 27 interactions with chain B, 10 interactions with chain A Hydrophobic interactions: B:K.68, B:K.70, B:T.186, B:V.209, B:K.215, B:L.218, B:L.218, B:P.228, B:V.229 Hydrogen bonds: B:L.72, B:T.186, B:V.206, B:E.207, B:E.208, B:E.208, B:V.209, B:K.215, B:C.217, B:C.217, A:A.137, A:R.139, A:R.139, A:K.140, A:N.290, A:N.290 Water bridges: B:K.68, B:G.71, B:G.71, A:R.292 Salt bridges: B:K.68, B:K.70, B:H.213, B:K.215, A:K.136, A:R.292 pi-Stacking: B:F.188 pi-Cation interactions: A:R.139 01.5: 28 residues within 4Å: Chain B: K.136, R.139, K.140, A.141, N.290, R.292, K.309 Chain C: K.68, L.69, K.70, G.71, L.72, N.184, F.185, T.186, F.188, L.205, V.206, E.207, E.208, V.209, H.213, M.214, K.215, C.217, L.218, P.228, V.229 37 PLIP interactions: 26 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: C:K.68, C:K.70, C:T.186, C:V.209, C:K.215, C:L.218, C:L.218, C:P.228, C:V.229 Hydrogen bonds: C:L.72, C:T.186, C:V.206, C:E.207, C:E.208, C:E.208, C:V.209, C:K.215, C:C.217, C:C.217, B:A.137, B:R.139, B:R.139, B:K.140, B:N.290, B:N.290 Water bridges: C:G.71, C:G.71, B:R.292, B:R.292 Salt bridges: C:K.68, C:K.70, C:H.213, C:K.215, B:K.136, B:R.292 pi-Stacking: C:F.188 pi-Cation interactions: B:R.139

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

NAG.2: 4 residues within 4Å: Chain A: P.121, F.152, N.153, D.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.171 NAG.4: 3 residues within 4Å: Chain B: P.121, N.153, D.171 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.171 NAG.6: 4 residues within 4Å: Chain C: P.121, F.152, N.153, D.171 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.171

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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