SMTL ID : 8v4s.1

Cryo-EM structure of the rat P2X7 receptor in the apo closed state purified in the absence of sodium

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 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.567, A:A.567, A:L.569, A:R.574, A:R.574, A:Q.587, A:S.589, A:G.590, 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 pi-Stacking: A:Y.550, A:F.591 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 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.567, B:A.567, B:L.569, B:R.574, B:R.574, B:Q.587, B:S.589, B:G.590, 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 pi-Stacking: B:Y.550, B:F.591 GDP.23: 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 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:A.567, C:A.567, C:L.569, C:R.574, C:R.574, C:Q.587, C:S.589, C:G.590, 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 pi-Stacking: C:Y.550, C:F.591

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: 7 residues within 4Å: Chain A: C.477, Q.478, C.479, G.480, 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: 7 residues within 4Å: Chain B: C.477, Q.478, C.479, G.480, 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.24: 5 residues within 4Å: Chain C: C.479, C.499, C.506, C.572 Ligands: ZN.25 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.25: 7 residues within 4Å: Chain C: C.477, Q.478, C.479, G.480, C.482, C.498 Ligands: ZN.24 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.477, C:C.479, C:C.482, C:C.498

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

NAG.4: 1 residues within 4Å: Chain A: N.202 No protein-ligand interaction detected (PLIP) NAG.5: 4 residues within 4Å: Chain A: R.183, S.184, E.186, N.187 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.186 Hydrogen bonds: A:E.186, A:E.186, A:N.187 NAG.6: 3 residues within 4Å: Chain A: N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:E.244 NAG.15: 1 residues within 4Å: Chain B: N.202 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: R.183, S.184, E.186, N.187 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:E.186 Hydrogen bonds: B:E.186, B:E.186, B:N.187 NAG.17: 3 residues within 4Å: Chain B: N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.241, B:E.244 NAG.26: 1 residues within 4Å: Chain C: N.202 No protein-ligand interaction detected (PLIP) NAG.27: 4 residues within 4Å: Chain C: R.183, S.184, E.186, N.187 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:E.186 Hydrogen bonds: C:E.186, C:E.186, C:N.187 NAG.28: 3 residues within 4Å: Chain C: N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.241, C:E.244

15 x PLM: PALMITIC ACID(Covalent)

PLM.7: 5 residues within 4Å: Chain A: L.353, N.356, T.357, S.360 Ligands: PLM.8 No protein-ligand interaction detected (PLIP) PLM.8: 5 residues within 4Å: Chain A: T.357, C.362, V.367 Ligands: PLM.7, PLM.9 No protein-ligand interaction detected (PLIP) PLM.9: 7 residues within 4Å: Chain A: T.357, Y.358, C.362, C.363, V.367 Ligands: PLM.8, PLM.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.358, A:Y.358 PLM.10: 4 residues within 4Å: Chain A: Y.358, V.367, C.374 Ligands: PLM.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.367 Hydrogen bonds: A:Y.358 PLM.11: 3 residues within 4Å: Chain A: I.354, Y.358, C.377 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.354 PLM.18: 5 residues within 4Å: Chain B: L.353, N.356, T.357, S.360 Ligands: PLM.19 No protein-ligand interaction detected (PLIP) PLM.19: 5 residues within 4Å: Chain B: T.357, C.362, V.367 Ligands: PLM.18, PLM.20 No protein-ligand interaction detected (PLIP) PLM.20: 7 residues within 4Å: Chain B: T.357, Y.358, C.362, C.363, V.367 Ligands: PLM.19, PLM.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.358, B:Y.358 PLM.21: 4 residues within 4Å: Chain B: Y.358, V.367, C.374 Ligands: PLM.20 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.367 Hydrogen bonds: B:Y.358 PLM.22: 3 residues within 4Å: Chain B: I.354, Y.358, C.377 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.354 PLM.29: 5 residues within 4Å: Chain C: L.353, N.356, T.357, S.360 Ligands: PLM.30 No protein-ligand interaction detected (PLIP) PLM.30: 5 residues within 4Å: Chain C: T.357, C.362, V.367 Ligands: PLM.29, PLM.31 No protein-ligand interaction detected (PLIP) PLM.31: 7 residues within 4Å: Chain C: T.357, Y.358, C.362, C.363, V.367 Ligands: PLM.30, PLM.32 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.358, C:Y.358 PLM.32: 4 residues within 4Å: Chain C: Y.358, V.367, C.374 Ligands: PLM.31 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.367 Hydrogen bonds: C:Y.358 PLM.33: 3 residues within 4Å: Chain C: I.354, Y.358, C.377 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.354

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oken, A.C. et al., High-affinity agonism at the P2X 7 receptor is mediated by three residues outside the orthosteric pocket. Nat Commun (2024)

Release Date

2024-08-14

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

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