SMTL ID : 8tr6.1

Cryo-EM structure of the rat P2X7 receptor in complex with the allosteric antagonist A438079

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x KE3: 3-{[(5R)-5-(2,3-dichlorophenyl)tetrazolidin-1-yl]methyl}pyridine(Non-covalent)

KE3.1: 16 residues within 4Å: Chain A: F.88, A.91, D.92, Y.93, T.94, L.95, F.103, M.105, Y.108, K.110, F.293, Y.295, K.297, I.310, A.312 Chain B: Y.298 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.310 pi-Stacking: A:F.88, A:Y.108 KE3.14: 16 residues within 4Å: Chain B: F.88, A.91, D.92, Y.93, T.94, L.95, F.103, M.105, Y.108, K.110, F.293, Y.295, K.297, I.310, A.312 Chain C: Y.298 2 PLIP interactions: 2 interactions with chain B pi-Stacking: B:F.88, B:Y.108 KE3.26: 16 residues within 4Å: Chain A: Y.298 Chain C: F.88, A.91, D.92, Y.93, T.94, L.95, F.103, M.105, Y.108, K.110, F.293, Y.295, K.297, I.310, A.312 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.310 pi-Stacking: C:F.88, C:Y.108

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

GDP.2: 18 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, Q.587, Y.588, S.589, G.590, F.591, K.592 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:Y.550, A:A.567, 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 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.15: 18 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, Q.587, Y.588, S.589, G.590, F.591, K.592 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:Y.550, B:A.567, 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 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.27: 18 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, Q.587, Y.588, S.589, G.590, F.591, K.592 18 PLIP interactions: 18 interactions with chain C Hydrogen bonds: C:Y.550, C:A.567, 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 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: 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.16: 7 residues within 4Å: Chain B: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.479, B:C.499, B:C.506, B:C.572 ZN.17: 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.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.477, B:C.479, B:C.482, B:C.498 ZN.28: 7 residues within 4Å: Chain C: C.479, N.481, C.499, C.506, I.507, C.572 Ligands: ZN.29 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.29: 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.28 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: 1 residues within 4Å: Chain A: N.202 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain A: R.183, S.184, E.186, N.187, R.230 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.186 Hydrogen bonds: A:E.186, A:E.186 NAG.7: 6 residues within 4Å: Chain A: R.178, P.179, N.241, T.243, E.244, V.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.241, A:E.244 NAG.18: 1 residues within 4Å: Chain B: N.202 No protein-ligand interaction detected (PLIP) NAG.19: 5 residues within 4Å: Chain B: R.183, S.184, E.186, N.187, R.230 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.186 Hydrogen bonds: B:E.186, B:E.186 NAG.20: 6 residues within 4Å: Chain B: R.178, P.179, N.241, T.243, E.244, V.247 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.241, B:E.244 NAG.30: 1 residues within 4Å: Chain C: N.202 No protein-ligand interaction detected (PLIP) NAG.31: 5 residues within 4Å: Chain C: R.183, S.184, E.186, N.187, R.230 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:E.186 Hydrogen bonds: C:E.186, C:E.186 NAG.32: 6 residues within 4Å: Chain C: R.178, P.179, N.241, T.243, E.244, V.247 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.241, C:E.244

15 x PLM: PALMITIC ACID(Covalent)

PLM.8: 6 residues within 4Å: Chain A: L.353, N.356, T.357, S.360 Ligands: PLM.9, PLM.10 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.353 PLM.9: 7 residues within 4Å: Chain A: T.357, C.362, C.363, R.366, V.367 Ligands: PLM.8, PLM.10 No protein-ligand interaction detected (PLIP) PLM.10: 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.8, PLM.9, PLM.11, PLM.12 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.354, A:T.357, A:Y.358, A:Y.358, A:V.367 PLM.11: 6 residues within 4Å: Chain A: Y.358, V.367, C.371, C.374 Ligands: PLM.10, PLM.12 No protein-ligand interaction detected (PLIP) PLM.12: 10 residues within 4Å: Chain A: Y.26, I.29, L.33, C.350, 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.29, A:I.354, A:Y.358 PLM.21: 6 residues within 4Å: Chain B: L.353, N.356, T.357, S.360 Ligands: PLM.22, PLM.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.353 PLM.22: 7 residues within 4Å: Chain B: T.357, C.362, C.363, R.366, V.367 Ligands: PLM.21, PLM.23 No protein-ligand interaction detected (PLIP) PLM.23: 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.21, PLM.22, PLM.24, PLM.25 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.354, B:T.357, B:Y.358, B:Y.358, B:V.367 PLM.24: 6 residues within 4Å: Chain B: Y.358, V.367, C.371, C.374 Ligands: PLM.23, PLM.25 No protein-ligand interaction detected (PLIP) PLM.25: 10 residues within 4Å: Chain B: Y.26, I.29, L.33, C.350, I.354, Y.358, C.377, N.380 Ligands: PLM.23, PLM.24 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.29, B:I.354, B:Y.358 PLM.33: 6 residues within 4Å: Chain C: L.353, N.356, T.357, S.360 Ligands: PLM.34, PLM.35 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.353 PLM.34: 7 residues within 4Å: Chain C: T.357, C.362, C.363, R.366, V.367 Ligands: PLM.33, PLM.35 No protein-ligand interaction detected (PLIP) PLM.35: 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.33, PLM.34, PLM.36, PLM.37 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.354, C:T.357, C:Y.358, C:Y.358, C:V.367 PLM.36: 6 residues within 4Å: Chain C: Y.358, V.367, C.371, C.374 Ligands: PLM.35, PLM.37 No protein-ligand interaction detected (PLIP) PLM.37: 10 residues within 4Å: Chain C: Y.26, I.29, L.33, C.350, I.354, Y.358, C.377, N.380 Ligands: PLM.35, PLM.36 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.29, C:I.354, C:Y.358

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

NA.13: 6 residues within 4Å: Chain A: G.338, S.342 Chain B: G.338, S.342 Chain C: G.338, S.342 6 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:G.338, B:S.342, A:S.342, C:S.342 Water bridges: B:S.342, A: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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