SMTL ID : 9e3q.1

Cryo-EM structure of the mouse P2X7 receptor in the apo closed state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 18 residues within 4Å: Chain A: S.543, R.546, H.547, Y.550, A.564, D.565, A.567, I.568, L.569, R.574, R.578, K.583, Q.587, Y.588, S.589, G.590, F.591, K.592 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.543, A:A.567, A:A.567, A:L.569, A:R.574, A:R.574, A:S.589, A:G.590, A:K.592, A:K.592, A:K.592 Salt bridges: A:R.546, A:R.546, A:H.547, A:H.547, A:R.578, A:K.583 GDP.12: 18 residues within 4Å: Chain B: S.543, R.546, H.547, Y.550, A.564, D.565, A.567, I.568, L.569, R.574, R.578, K.583, Q.587, Y.588, S.589, G.590, F.591, K.592 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:S.543, B:A.567, B:A.567, B:L.569, B:R.574, B:R.574, B:S.589, B:G.590, B:K.592, B:K.592, B:K.592 Salt bridges: B:R.546, B:R.546, B:H.547, B:H.547, B:R.578, B:K.583 GDP.22: 18 residues within 4Å: Chain C: S.543, R.546, H.547, Y.550, A.564, D.565, A.567, I.568, L.569, R.574, R.578, K.583, Q.587, Y.588, S.589, G.590, F.591, K.592 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:S.543, C:A.567, C:A.567, C:L.569, C:R.574, C:R.574, C:S.589, C:G.590, C:K.592, C:K.592, C:K.592 Salt bridges: C:R.546, C:R.546, C:H.547, C:H.547, C:R.578, C:K.583

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.479, C.499, C.506, C.572 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.479, A:C.499, A:C.506, A:C.572 ZN.3: 6 residues within 4Å: Chain A: C.477, Q.478, C.479, C.482, C.498 Ligands: ZN.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.477, A:C.479, A:C.482, A:C.498 ZN.13: 5 residues within 4Å: Chain B: C.479, C.499, C.506, C.572 Ligands: ZN.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.479, B:C.499, B:C.506, B:C.572 ZN.14: 6 residues within 4Å: Chain B: C.477, Q.478, C.479, C.482, C.498 Ligands: ZN.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.477, B:C.479, B:C.482, B:C.498 ZN.23: 5 residues within 4Å: Chain C: C.479, C.499, C.506, C.572 Ligands: ZN.24 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.24: 6 residues within 4Å: Chain C: C.477, Q.478, C.479, C.482, C.498 Ligands: ZN.23 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.477, C:C.479, C:C.482, C:C.498

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

NAG.4: 4 residues within 4Å: Chain A: R.183, S.184, E.186, N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.187 NAG.5: 3 residues within 4Å: Chain A: N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.244, A:E.244 NAG.15: 4 residues within 4Å: Chain B: R.183, S.184, E.186, N.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.187 NAG.16: 3 residues within 4Å: Chain B: N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.244, B:E.244 NAG.25: 4 residues within 4Å: Chain C: R.183, S.184, E.186, N.187 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.187 NAG.26: 3 residues within 4Å: Chain C: N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.244, C:E.244

15 x PLM: PALMITIC ACID(Covalent)

PLM.6: 10 residues within 4Å: Chain A: L.353, L.354, T.357, Y.358, S.360, F.362, C.363, V.367 Ligands: PLM.9, PLM.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.353, A:L.354, A:Y.358, A:F.362, A:V.367 Hydrogen bonds: A:S.360 PLM.7: 3 residues within 4Å: Chain A: V.367, C.371 Ligands: PLM.9 No protein-ligand interaction detected (PLIP) PLM.8: 2 residues within 4Å: Chain A: C.373 Ligands: PLM.9 No protein-ligand interaction detected (PLIP) PLM.9: 6 residues within 4Å: Chain A: Y.358, V.367, C.374 Ligands: PLM.6, PLM.7, PLM.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.358 PLM.10: 8 residues within 4Å: Chain A: N.25, V.29, C.350, L.354, Y.358, C.377, N.380 Ligands: PLM.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.29, A:L.354 Hydrogen bonds: A:N.380 PLM.17: 10 residues within 4Å: Chain B: L.353, L.354, T.357, Y.358, S.360, F.362, C.363, V.367 Ligands: PLM.20, PLM.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.353, B:L.354, B:Y.358, B:F.362, B:V.367 Hydrogen bonds: B:S.360 PLM.18: 3 residues within 4Å: Chain B: V.367, C.371 Ligands: PLM.20 No protein-ligand interaction detected (PLIP) PLM.19: 2 residues within 4Å: Chain B: C.373 Ligands: PLM.20 No protein-ligand interaction detected (PLIP) PLM.20: 6 residues within 4Å: Chain B: Y.358, V.367, C.374 Ligands: PLM.17, PLM.18, PLM.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.358 PLM.21: 8 residues within 4Å: Chain B: N.25, V.29, C.350, L.354, Y.358, C.377, N.380 Ligands: PLM.17 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.29, B:L.354 Hydrogen bonds: B:N.380 PLM.27: 10 residues within 4Å: Chain C: L.353, L.354, T.357, Y.358, S.360, F.362, C.363, V.367 Ligands: PLM.30, PLM.31 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.353, C:L.354, C:Y.358, C:F.362, C:V.367 Hydrogen bonds: C:S.360 PLM.28: 3 residues within 4Å: Chain C: V.367, C.371 Ligands: PLM.30 No protein-ligand interaction detected (PLIP) PLM.29: 2 residues within 4Å: Chain C: C.373 Ligands: PLM.30 No protein-ligand interaction detected (PLIP) PLM.30: 6 residues within 4Å: Chain C: Y.358, V.367, C.374 Ligands: PLM.27, PLM.28, PLM.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.358 PLM.31: 8 residues within 4Å: Chain C: N.25, V.29, C.350, L.354, Y.358, C.377, N.380 Ligands: PLM.27 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.29, C:L.354 Hydrogen bonds: C:N.380

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 6 residues within 4Å: Chain A: G.338, S.342 Chain B: G.338, S.342 Chain C: G.338, S.342 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:S.342, B:S.342, B:S.342, A:S.342 Water bridges: C:S.342, B:S.342, A:S.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oken, A.C. et al., A polycyclic scaffold identified by structure-based drug design effectively inhibits the human P2X7 receptor. Nat Commun (2025)

Release Date

2025-09-24

Peptides

P2X purinoceptor 7: 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 7