SMTL ID : 8trb.1

Cryo-EM structure of the rat P2X7 receptor in complex with the allosteric antagonist JNJ47965567

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x 7RV: N-{[4-(4-phenylpiperazin-1-yl)oxan-4-yl]methyl}-2-(phenylsulfanyl)pyridine-3-carboxamide(Non-covalent)

7RV.1: 28 residues within 4Å: Chain A: G.86, I.87, F.88, A.91, D.92, Y.93, T.94, L.95, P.96, F.103, M.105, Y.108, K.110, F.293, Y.295, K.297, I.310, A.312 Chain B: L.95, Q.116, W.167, F.293, R.294, Y.295, Y.298, E.305 Ligands: 7RV.13, 7RV.24 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.96, A:Y.295, A:I.310, A:I.310, B:W.167, B:Y.298 Hydrogen bonds: A:D.92, A:K.110, A:K.297 pi-Stacking: A:Y.108, B:Y.295 7RV.13: 28 residues within 4Å: Chain B: G.86, I.87, F.88, A.91, D.92, Y.93, T.94, L.95, P.96, F.103, M.105, Y.108, K.110, F.293, Y.295, K.297, I.310, A.312 Chain C: L.95, Q.116, W.167, F.293, R.294, Y.295, Y.298, E.305 Ligands: 7RV.1, 7RV.24 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:P.96, B:Y.295, B:I.310, B:I.310, C:W.167, C:Y.298 Hydrogen bonds: B:D.92, B:K.110, B:K.297 pi-Stacking: B:Y.108, C:Y.295 7RV.24: 28 residues within 4Å: Chain A: L.95, Q.116, W.167, F.293, R.294, Y.295, Y.298, E.305 Chain C: G.86, I.87, F.88, A.91, D.92, Y.93, T.94, L.95, P.96, F.103, M.105, Y.108, K.110, F.293, Y.295, K.297, I.310, A.312 Ligands: 7RV.1, 7RV.13 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:P.96, C:Y.295, C:I.310, C:I.310, A:W.167, A:Y.298 Hydrogen bonds: C:D.92, C:K.110, C:K.297 pi-Stacking: C:Y.108, A:Y.295

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

GDP.2: 20 residues within 4Å: Chain A: S.543, R.546, H.547, Y.550, R.551, A.554, 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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.550, A:A.567, A:A.567, A:L.569, A:R.574, A:R.574, A:S.589, A:S.589, A:G.590 Salt bridges: A:R.546, A:R.546, A:H.547, A:H.547, A:R.578, A:K.583 pi-Stacking: A:F.591 GDP.14: 20 residues within 4Å: Chain B: S.543, R.546, H.547, Y.550, R.551, A.554, 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:Y.550, B:A.567, B:A.567, B:L.569, B:R.574, B:R.574, B:S.589, B:S.589, B:G.590 Salt bridges: B:R.546, B:R.546, B:H.547, B:H.547, B:R.578, B:K.583 pi-Stacking: B:F.591 GDP.25: 20 residues within 4Å: Chain C: S.543, R.546, H.547, Y.550, R.551, A.554, 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 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.550, C:A.567, C:A.567, C:L.569, C:R.574, C:R.574, C:S.589, C:S.589, C:G.590 Salt bridges: C:R.546, C:R.546, C:H.547, C:H.547, C:R.578, 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: 9 residues within 4Å: Chain A: C.477, Q.478, C.479, G.480, N.481, C.482, C.498, C.499 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: 9 residues within 4Å: Chain B: C.477, Q.478, C.479, G.480, N.481, C.482, C.498, C.499 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.26: 7 residues within 4Å: Chain C: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.27 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.27: 9 residues within 4Å: Chain C: C.477, Q.478, C.479, G.480, N.481, C.482, C.498, C.499 Ligands: ZN.26 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.5: 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:R.183, A:E.186 Hydrogen bonds: A:E.186, A:E.186 NAG.6: 4 residues within 4Å: Chain A: R.178, N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.244, A:E.244, A:E.244 NAG.17: 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:R.183, B:E.186 Hydrogen bonds: B:E.186, B:E.186 NAG.18: 4 residues within 4Å: Chain B: R.178, N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.244, B:E.244, B:E.244 NAG.28: 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:R.183, C:E.186 Hydrogen bonds: C:E.186, C:E.186 NAG.29: 4 residues within 4Å: Chain C: R.178, N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.244, C:E.244, C:E.244

15 x PLM: PALMITIC ACID(Covalent)

PLM.7: 6 residues within 4Å: Chain A: L.353, N.356, T.357, S.360 Ligands: PLM.8, PLM.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.353 PLM.8: 7 residues within 4Å: Chain A: T.357, S.360, C.362, R.366, V.367 Ligands: PLM.7, PLM.9 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.357 PLM.9: 13 residues within 4Å: Chain A: L.353, I.354, T.357, Y.358, S.360, C.362, C.363, V.367, Y.368 Ligands: PLM.7, PLM.8, PLM.10, PLM.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.354, A:Y.358 Hydrogen bonds: A:C.363 PLM.10: 6 residues within 4Å: Chain A: Y.358, V.367, C.371, C.374 Ligands: PLM.9, PLM.11 No protein-ligand interaction detected (PLIP) PLM.11: 12 residues within 4Å: Chain A: N.25, Y.26, I.29, L.33, C.350, I.354, Y.358, P.376, C.377, N.380 Ligands: PLM.9, PLM.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.29 PLM.19: 6 residues within 4Å: Chain B: L.353, N.356, T.357, S.360 Ligands: PLM.20, PLM.21 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.353 PLM.20: 7 residues within 4Å: Chain B: T.357, S.360, C.362, R.366, V.367 Ligands: PLM.19, PLM.21 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.357 PLM.21: 13 residues within 4Å: Chain B: L.353, I.354, T.357, Y.358, S.360, C.362, C.363, V.367, Y.368 Ligands: PLM.19, PLM.20, PLM.22, PLM.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.354, B:Y.358 Hydrogen bonds: B:C.363 PLM.22: 6 residues within 4Å: Chain B: Y.358, V.367, C.371, C.374 Ligands: PLM.21, PLM.23 No protein-ligand interaction detected (PLIP) PLM.23: 12 residues within 4Å: Chain B: N.25, Y.26, I.29, L.33, C.350, I.354, Y.358, P.376, C.377, N.380 Ligands: PLM.21, PLM.22 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.29 PLM.30: 6 residues within 4Å: Chain C: L.353, N.356, T.357, S.360 Ligands: PLM.31, PLM.32 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.353 PLM.31: 7 residues within 4Å: Chain C: T.357, S.360, C.362, R.366, V.367 Ligands: PLM.30, PLM.32 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.357 PLM.32: 13 residues within 4Å: Chain C: L.353, I.354, T.357, Y.358, S.360, C.362, C.363, V.367, Y.368 Ligands: PLM.30, PLM.31, PLM.33, PLM.34 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.354, C:Y.358 Hydrogen bonds: C:C.363 PLM.33: 6 residues within 4Å: Chain C: Y.358, V.367, C.371, C.374 Ligands: PLM.32, PLM.34 No protein-ligand interaction detected (PLIP) PLM.34: 12 residues within 4Å: Chain C: N.25, Y.26, I.29, L.33, C.350, I.354, Y.358, P.376, C.377, N.380 Ligands: PLM.32, PLM.33 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.29

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

NA.12: 6 residues within 4Å: Chain A: G.338, S.342 Chain B: G.338, S.342 Chain C: G.338, S.342 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:S.342, B:S.342, C:S.342, C:S.342

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oken, A.C. et al., P2X 7 receptors exhibit at least three modes of allosteric antagonism. Sci Adv (2024)

Release Date

2024-10-16

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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