SMTL ID : 8trk.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x KFM: 4,4',4''-[methanetriyltris(4,1-phenyleneazanediyl)]tri(benzene-1-sulfonic acid)(Non-covalent)

KFM.1: 28 residues within 4Å: Chain A: F.88, Y.93, T.94, L.95, P.96, L.97, S.101, F.102, F.103, M.105, Y.108, K.110, Y.291, F.293, Y.295, K.297, I.310, R.316 Chain B: D.92, Y.93, P.96, L.97, Q.98, G.99, Y.295, K.297 Ligands: KFM.15, KFM.29 21 PLIP interactions: 17 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.93, A:T.94, A:P.96, A:F.293, A:F.293, A:F.293, A:Y.295, A:Y.295, A:Y.295, B:P.96, B:L.97 Hydrogen bonds: A:T.94, A:S.101, A:Y.291, B:Q.98 Salt bridges: A:K.110, A:K.297, A:R.316, B:K.297 pi-Stacking: A:F.88, A:Y.295 KFM.15: 28 residues within 4Å: Chain B: F.88, Y.93, T.94, L.95, P.96, L.97, S.101, F.102, F.103, M.105, Y.108, K.110, Y.291, F.293, Y.295, K.297, I.310, R.316 Chain C: D.92, Y.93, P.96, L.97, Q.98, G.99, Y.295, K.297 Ligands: KFM.1, KFM.29 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:Y.93, B:T.94, B:P.96, B:F.293, B:F.293, B:F.293, B:Y.295, B:Y.295, B:Y.295, C:P.96, C:L.97 Hydrogen bonds: B:T.94, B:S.101, B:Y.291, C:Q.98 Salt bridges: B:K.110, B:K.297, B:R.316, C:K.297 pi-Stacking: B:F.88, B:Y.295 KFM.29: 28 residues within 4Å: Chain A: D.92, Y.93, P.96, L.97, Q.98, G.99, Y.295, K.297 Chain C: F.88, Y.93, T.94, L.95, P.96, L.97, S.101, F.102, F.103, M.105, Y.108, K.110, Y.291, F.293, Y.295, K.297, I.310, R.316 Ligands: KFM.1, KFM.15 21 PLIP interactions: 17 interactions with chain C, 4 interactions with chain A Hydrophobic interactions: C:Y.93, C:T.94, C:P.96, C:F.293, C:F.293, C:F.293, C:Y.295, C:Y.295, C:Y.295, A:P.96, A:L.97 Hydrogen bonds: C:T.94, C:S.101, C:Y.291, A:Q.98 Salt bridges: C:K.110, C:K.297, C:R.316, A:K.297 pi-Stacking: C:F.88, C:Y.295

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

GDP.2: 18 residues within 4Å: Chain A: R.546, H.547, Y.550, A.564, D.565, F.566, 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:H.547, 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 Water bridges: A:S.589, A:S.589 Salt bridges: A:R.546, A:R.546, A:H.547, A:R.578, A:K.583 pi-Stacking: A:F.591 GDP.16: 18 residues within 4Å: Chain B: R.546, H.547, Y.550, A.564, D.565, F.566, 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:H.547, 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 Water bridges: B:S.589, B:S.589 Salt bridges: B:R.546, B:R.546, B:H.547, B:R.578, B:K.583 pi-Stacking: B:F.591 GDP.30: 18 residues within 4Å: Chain C: R.546, H.547, Y.550, A.564, D.565, F.566, 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:H.547, 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 Water bridges: C:S.589, C:S.589 Salt bridges: C:R.546, C:R.546, 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: 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.17: 7 residues within 4Å: Chain B: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.479, B:C.499, B:C.506, B:C.572 ZN.18: 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.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.477, B:C.479, B:C.482, B:C.498 ZN.31: 7 residues within 4Å: Chain C: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.32 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.32: 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.31 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.477, C:C.479, C:C.482, C:C.498

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

NAG.5: 1 residues within 4Å: Chain A: N.202 No protein-ligand interaction detected (PLIP) NAG.6: 4 residues within 4Å: Chain A: N.213, S.215, C.216, N.223 No protein-ligand interaction detected (PLIP) NAG.7: 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.8: 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.9: 4 residues within 4Å: Chain A: N.284, E.285, S.286 Chain B: I.214 No protein-ligand interaction detected (PLIP) NAG.19: 1 residues within 4Å: Chain B: N.202 No protein-ligand interaction detected (PLIP) NAG.20: 4 residues within 4Å: Chain B: N.213, S.215, C.216, N.223 No protein-ligand interaction detected (PLIP) NAG.21: 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.22: 3 residues within 4Å: Chain B: N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.244, B:E.244 Water bridges: B:T.243 NAG.23: 4 residues within 4Å: Chain B: N.284, E.285, S.286 Chain C: I.214 No protein-ligand interaction detected (PLIP) NAG.33: 1 residues within 4Å: Chain C: N.202 No protein-ligand interaction detected (PLIP) NAG.34: 4 residues within 4Å: Chain C: N.213, S.215, C.216, N.223 No protein-ligand interaction detected (PLIP) NAG.35: 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.36: 3 residues within 4Å: Chain C: N.241, T.243, E.244 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.244, C:E.244 Water bridges: C:T.243 NAG.37: 4 residues within 4Å: Chain A: I.214 Chain C: N.284, E.285, S.286 No protein-ligand interaction detected (PLIP)

15 x PLM: PALMITIC ACID(Covalent)

PLM.10: 7 residues within 4Å: Chain A: L.353, N.356, T.357, S.360, C.362 Ligands: 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: T.357, C.362, C.363, R.366, V.367 Ligands: PLM.10, PLM.12 No protein-ligand interaction detected (PLIP) PLM.12: 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.10, PLM.11, PLM.13, PLM.14 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.354, A:Y.358, A:Y.358 PLM.13: 6 residues within 4Å: Chain A: Y.358, V.367, Y.368, C.371, C.374 Ligands: PLM.12 No protein-ligand interaction detected (PLIP) PLM.14: 9 residues within 4Å: Chain A: N.25, Y.26, I.29, L.33, I.354, Y.358, C.377, N.380 Ligands: PLM.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.358 Hydrogen bonds: A:Y.358 PLM.24: 7 residues within 4Å: Chain B: L.353, N.356, T.357, S.360, C.362 Ligands: PLM.25, PLM.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.357 PLM.25: 7 residues within 4Å: Chain B: T.357, C.362, C.363, R.366, V.367 Ligands: PLM.24, PLM.26 No protein-ligand interaction detected (PLIP) PLM.26: 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.24, PLM.25, PLM.27, PLM.28 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.354, B:Y.358, B:Y.358 PLM.27: 6 residues within 4Å: Chain B: Y.358, V.367, Y.368, C.371, C.374 Ligands: PLM.26 No protein-ligand interaction detected (PLIP) PLM.28: 9 residues within 4Å: Chain B: N.25, Y.26, I.29, L.33, I.354, Y.358, C.377, N.380 Ligands: PLM.26 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.358 Hydrogen bonds: B:Y.358 PLM.38: 7 residues within 4Å: Chain C: L.353, N.356, T.357, S.360, C.362 Ligands: PLM.39, PLM.40 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.357 PLM.39: 7 residues within 4Å: Chain C: T.357, C.362, C.363, R.366, V.367 Ligands: PLM.38, PLM.40 No protein-ligand interaction detected (PLIP) PLM.40: 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.38, PLM.39, PLM.41, PLM.42 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.354, C:Y.358, C:Y.358 PLM.41: 6 residues within 4Å: Chain C: Y.358, V.367, Y.368, C.371, C.374 Ligands: PLM.40 No protein-ligand interaction detected (PLIP) PLM.42: 9 residues within 4Å: Chain C: N.25, Y.26, I.29, L.33, I.354, Y.358, C.377, N.380 Ligands: PLM.40 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.358 Hydrogen bonds: C:Y.358

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
C

C
B

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor 7

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