SMTL ID : 8tr7.1

Cryo-EM structure of the rat P2X7 receptor in complex with the allosteric antagonist A839977

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

3 x KDU: (1P)-1-(2,3-dichlorophenyl)-N-({2-[(pyridin-2-yl)oxy]phenyl}methyl)-1H-tetrazol-5-amine(Non-covalent)

KDU.1: 20 residues within 4Å: Chain A: G.86, I.87, F.88, A.91, D.92, Y.93, T.94, L.95, F.103, M.105, Y.108, K.110, F.293, Y.295, I.310, A.312 Chain B: Q.116, W.167, Y.298, E.305 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.95, B:W.167 Hydrogen bonds: A:D.92 Water bridges: A:K.110 pi-Stacking: A:F.88, A:Y.108 KDU.13: 20 residues within 4Å: Chain B: G.86, I.87, F.88, A.91, D.92, Y.93, T.94, L.95, F.103, M.105, Y.108, K.110, F.293, Y.295, I.310, A.312 Chain C: Q.116, W.167, Y.298, E.305 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.95, C:W.167 Hydrogen bonds: B:D.92 Water bridges: B:K.110 pi-Stacking: B:F.88, B:Y.108 KDU.24: 20 residues within 4Å: Chain A: Q.116, W.167, Y.298, E.305 Chain C: G.86, I.87, F.88, A.91, D.92, Y.93, T.94, L.95, F.103, M.105, Y.108, K.110, F.293, Y.295, I.310, A.312 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.95, A:W.167 Hydrogen bonds: C:D.92 Water bridges: C:K.110 pi-Stacking: C:F.88, C:Y.108

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

GDP.2: 17 residues within 4Å: Chain A: 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 15 PLIP interactions: 15 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 Salt bridges: A:R.546, A:R.546, A:H.547, A:R.578, A:K.583 GDP.14: 17 residues within 4Å: Chain B: 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 15 PLIP interactions: 15 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 Salt bridges: B:R.546, B:R.546, B:H.547, B:R.578, B:K.583 GDP.25: 17 residues within 4Å: Chain C: 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 15 PLIP interactions: 15 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 Salt bridges: C:R.546, C:R.546, C:H.547, C:R.578, C:K.583

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: W.476, C.477, Q.478, C.479, 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: W.476, C.477, Q.478, C.479, 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.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: 10 residues within 4Å: Chain C: W.476, C.477, Q.478, C.479, N.481, C.482, C.498, C.499, C.572 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.187 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:N.241, A:E.244, A:E.244 NAG.17: 5 residues within 4Å: Chain B: R.183, S.184, E.186, N.187, R.230 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.187 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:N.241, B:E.244, B:E.244 NAG.28: 5 residues within 4Å: Chain C: R.183, S.184, E.186, N.187, R.230 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.187 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:N.241, C:E.244, C:E.244

15 x PLM: PALMITIC ACID(Covalent)

PLM.7: 7 residues within 4Å: Chain A: V.349, D.352, L.353, N.356, T.357, S.360 Ligands: PLM.8 No protein-ligand interaction detected (PLIP) PLM.8: 7 residues within 4Å: Chain A: T.357, S.360, C.362, C.363, V.367 Ligands: PLM.7, PLM.9 No protein-ligand interaction detected (PLIP) PLM.9: 9 residues within 4Å: Chain A: L.353, I.354, T.357, Y.358, C.363, V.367 Ligands: PLM.8, PLM.10, PLM.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.358, A:Y.358 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: 9 residues within 4Å: Chain A: Y.26, I.29, L.33, I.354, Y.358, C.377, N.380 Ligands: PLM.9, PLM.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.354 Hydrogen bonds: A:N.380 PLM.19: 7 residues within 4Å: Chain B: V.349, D.352, L.353, N.356, T.357, S.360 Ligands: PLM.20 No protein-ligand interaction detected (PLIP) PLM.20: 7 residues within 4Å: Chain B: T.357, S.360, C.362, C.363, V.367 Ligands: PLM.19, PLM.21 No protein-ligand interaction detected (PLIP) PLM.21: 9 residues within 4Å: Chain B: L.353, I.354, T.357, Y.358, C.363, V.367 Ligands: PLM.20, PLM.22, PLM.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.358, B:Y.358 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: 9 residues within 4Å: Chain B: Y.26, I.29, L.33, I.354, Y.358, C.377, N.380 Ligands: PLM.21, PLM.22 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.354 Hydrogen bonds: B:N.380 PLM.30: 7 residues within 4Å: Chain C: V.349, D.352, L.353, N.356, T.357, S.360 Ligands: PLM.31 No protein-ligand interaction detected (PLIP) PLM.31: 7 residues within 4Å: Chain C: T.357, S.360, C.362, C.363, V.367 Ligands: PLM.30, PLM.32 No protein-ligand interaction detected (PLIP) PLM.32: 9 residues within 4Å: Chain C: L.353, I.354, T.357, Y.358, C.363, V.367 Ligands: PLM.31, PLM.33, PLM.34 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.358, C:Y.358 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: 9 residues within 4Å: Chain C: Y.26, I.29, L.33, I.354, Y.358, C.377, N.380 Ligands: PLM.32, PLM.33 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.354 Hydrogen bonds: C:N.380

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 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: 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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