SMTL ID : 8trj.1

Cryo-EM structure of the rat P2X7 receptor in complex with the high-affinity agonist BzATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x KD9: 3'-O-(4-benzoylbenzoyl)adenosine 5'-(tetrahydrogen triphosphate)(Non-covalent)

KD9.1: 18 residues within 4Å: Chain A: R.125, P.142, Q.143, K.145, F.288, P.289, N.292, R.294, K.311 Chain C: K.64, V.65, K.66, T.189, V.190, L.191, K.193, I.214, I.228 25 PLIP interactions: 11 interactions with chain C, 14 interactions with chain A Hydrogen bonds: C:K.66, C:T.189, C:L.191, A:R.125, A:R.125, A:Q.143, A:N.292 Water bridges: C:K.193, C:K.193, A:R.294, A:R.294, A:R.294 Salt bridges: C:K.64, C:K.64, C:K.64, C:K.66, C:K.193, A:R.125, A:R.125, A:K.145, A:R.294, A:K.311, A:K.311 pi-Cation interactions: C:K.66 Hydrophobic interactions: A:R.125 KD9.13: 18 residues within 4Å: Chain A: K.64, V.65, K.66, T.189, V.190, L.191, K.193, I.214, I.228 Chain B: R.125, P.142, Q.143, K.145, F.288, P.289, N.292, R.294, K.311 25 PLIP interactions: 14 interactions with chain B, 11 interactions with chain A Hydrophobic interactions: B:R.125 Hydrogen bonds: B:R.125, B:R.125, B:Q.143, B:N.292, A:K.66, A:T.189, A:L.191 Water bridges: B:R.294, B:R.294, B:R.294, A:K.193, A:K.193 Salt bridges: B:R.125, B:R.125, B:K.145, B:R.294, B:K.311, B:K.311, A:K.64, A:K.64, A:K.64, A:K.66, A:K.193 pi-Cation interactions: A:K.66 KD9.25: 18 residues within 4Å: Chain B: K.64, V.65, K.66, T.189, V.190, L.191, K.193, I.214, I.228 Chain C: R.125, P.142, Q.143, K.145, F.288, P.289, N.292, R.294, K.311 25 PLIP interactions: 11 interactions with chain B, 14 interactions with chain C Hydrogen bonds: B:K.66, B:T.189, B:L.191, C:R.125, C:R.125, C:Q.143, C:N.292 Water bridges: B:K.193, B:K.193, C:R.294, C:R.294, C:R.294 Salt bridges: B:K.64, B:K.64, B:K.64, B:K.66, B:K.193, C:R.125, C:R.125, C:K.145, C:R.294, C:K.311, C:K.311 pi-Cation interactions: B:K.66 Hydrophobic interactions: C:R.125

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

GDP.2: 17 residues within 4Å: Chain A: R.546, H.547, Y.550, A.554, A.564, D.565, A.567, I.568, L.569, R.574, R.578, K.583, Y.588, S.589, G.590, F.591, K.592 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:A.567, A:A.567, A:L.569, A:R.574, A:R.574, A:R.578, A:S.589, A:K.592, A:K.592 Salt bridges: A:R.546, A:R.546, A:H.547, A:K.583 pi-Stacking: A:F.591 GDP.14: 17 residues within 4Å: Chain B: R.546, H.547, Y.550, A.554, A.564, D.565, A.567, I.568, L.569, R.574, R.578, K.583, Y.588, S.589, G.590, F.591, K.592 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.567, B:A.567, B:L.569, B:R.574, B:R.574, B:R.578, B:S.589, B:K.592, B:K.592 Salt bridges: B:R.546, B:R.546, B:H.547, B:K.583 pi-Stacking: B:F.591 GDP.26: 17 residues within 4Å: Chain C: R.546, H.547, Y.550, A.554, A.564, D.565, A.567, I.568, L.569, R.574, R.578, K.583, Y.588, S.589, G.590, F.591, K.592 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:A.567, C:A.567, C:L.569, C:R.574, C:R.574, C:R.578, C:S.589, C:K.592, C:K.592 Salt bridges: C:R.546, C:R.546, C:H.547, C:K.583 pi-Stacking: C:F.591

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 7 residues within 4Å: Chain A: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.479, A:C.499, A:C.506, A:C.572 ZN.4: 10 residues within 4Å: Chain A: C.477, Q.478, C.479, G.480, N.481, C.482, C.498, C.499, C.572 Ligands: ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.477, A:C.479, A:C.482, A:C.498 ZN.15: 7 residues within 4Å: Chain B: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.479, B:C.499, B:C.506, B:C.572 ZN.16: 10 residues within 4Å: Chain B: C.477, Q.478, C.479, G.480, N.481, C.482, C.498, C.499, C.572 Ligands: ZN.15 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.477, B:C.479, B:C.482, B:C.498 ZN.27: 7 residues within 4Å: Chain C: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.28 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.28: 10 residues within 4Å: Chain C: C.477, Q.478, C.479, G.480, N.481, C.482, C.498, C.499, C.572 Ligands: ZN.27 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.5: 3 residues within 4Å: Chain A: N.213, S.215, C.216 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain A: R.183, S.184, E.186, N.187, R.230 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.7: 3 residues within 4Å: Chain A: N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.243, A:T.243, A:E.244 NAG.17: 3 residues within 4Å: Chain B: N.213, S.215, C.216 No protein-ligand interaction detected (PLIP) NAG.18: 5 residues within 4Å: Chain B: R.183, S.184, E.186, N.187, R.230 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.19: 3 residues within 4Å: Chain B: N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.243, B:T.243, B:E.244 NAG.29: 3 residues within 4Å: Chain C: N.213, S.215, C.216 No protein-ligand interaction detected (PLIP) NAG.30: 5 residues within 4Å: Chain C: R.183, S.184, E.186, N.187, R.230 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.31: 3 residues within 4Å: Chain C: N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.243, C:T.243, C:E.244

15 x PLM: PALMITIC ACID(Covalent)

PLM.8: 7 residues within 4Å: Chain A: N.356, T.357, A.359, S.360 Chain C: W.31 Ligands: PLM.9, PLM.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:S.360 PLM.9: 8 residues within 4Å: Chain A: T.357, S.360, C.362, C.363, R.366, V.367 Ligands: PLM.8, PLM.10 No protein-ligand interaction detected (PLIP) PLM.10: 9 residues within 4Å: Chain A: T.357, Y.358, S.360, C.363, V.367 Ligands: PLM.8, PLM.9, PLM.11, PLM.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.357 PLM.11: 7 residues within 4Å: Chain A: Y.358, V.367, C.371, C.373, C.374 Ligands: PLM.10, PLM.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.367 PLM.12: 8 residues within 4Å: Chain A: N.25, I.29, I.354, Y.358, C.377, N.380 Ligands: PLM.10, PLM.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.354, A:I.354 Hydrogen bonds: A:N.25 PLM.20: 8 residues within 4Å: Chain A: W.31, H.34 Chain B: N.356, T.357, A.359, S.360 Ligands: PLM.21, PLM.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:S.360 PLM.21: 8 residues within 4Å: Chain B: T.357, S.360, C.362, C.363, R.366, V.367 Ligands: PLM.20, PLM.22 No protein-ligand interaction detected (PLIP) PLM.22: 9 residues within 4Å: Chain B: T.357, Y.358, S.360, C.363, V.367 Ligands: PLM.20, PLM.21, PLM.23, PLM.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.357 PLM.23: 7 residues within 4Å: Chain B: Y.358, V.367, C.371, C.373, C.374 Ligands: PLM.22, PLM.24 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:V.367 PLM.24: 8 residues within 4Å: Chain B: N.25, I.29, I.354, Y.358, C.377, N.380 Ligands: PLM.22, PLM.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.354, B:I.354 Hydrogen bonds: B:N.25 PLM.32: 8 residues within 4Å: Chain B: W.31, H.34 Chain C: N.356, T.357, A.359, S.360 Ligands: PLM.33, PLM.34 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:S.360 PLM.33: 8 residues within 4Å: Chain C: T.357, S.360, C.362, C.363, R.366, V.367 Ligands: PLM.32, PLM.34 No protein-ligand interaction detected (PLIP) PLM.34: 9 residues within 4Å: Chain C: T.357, Y.358, S.360, C.363, V.367 Ligands: PLM.32, PLM.33, PLM.35, PLM.36 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.357 PLM.35: 7 residues within 4Å: Chain C: Y.358, V.367, C.371, C.373, C.374 Ligands: PLM.34, PLM.36 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.367 PLM.36: 8 residues within 4Å: Chain C: N.25, I.29, I.354, Y.358, C.377, N.380 Ligands: PLM.34, PLM.35 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.354, C:I.354 Hydrogen bonds: C:N.25

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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