SMTL ID : 6u9w.1

Cryo electron microscopy structure of the ATP-gated rat P2X7 ion channel in the ATP-bound, open state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 4 residues within 4Å: Chain A: P.179, N.241, T.243, E.244 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: R.183, S.184, E.186, N.187 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: P.179, N.241, T.243, E.244 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain B: R.183, S.184, E.186, N.187 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: P.179, N.241, T.243, E.244 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: R.183, S.184, E.186, N.187 No protein-ligand interaction detected (PLIP)

6 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: C.479, N.481, C.499, C.506, I.507, C.572 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.479, A:C.499, A:C.506, A:C.572 ZN.8: 7 residues within 4Å: Chain A: C.477, Q.478, C.479, G.480, N.481, C.482, C.498 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.477, A:C.479, A:C.482, A:C.498 ZN.18: 6 residues within 4Å: Chain B: C.479, N.481, C.499, C.506, I.507, C.572 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.479, B:C.499, B:C.506, B:C.572 ZN.19: 7 residues within 4Å: Chain B: C.477, Q.478, C.479, G.480, N.481, C.482, C.498 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.477, B:C.479, B:C.482, B:C.498 ZN.30: 6 residues within 4Å: Chain C: C.479, N.481, C.499, C.506, I.507, C.572 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.479, C:C.499, C:C.506, C:C.572 ZN.31: 7 residues within 4Å: Chain C: C.477, Q.478, C.479, G.480, N.481, C.482, C.498 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.477, C:C.479, C:C.482, C:C.498

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

GDP.9: 18 residues within 4Å: Chain A: S.543, R.546, H.547, Y.550, A.564, D.565, F.566, A.567, I.568, L.569, R.574, R.578, K.583, Y.588, S.589, G.590, F.591, K.592 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:H.547, A:Y.550, A:A.567, A:A.567, A:L.569, A:R.574, A:S.589, A:K.592 Salt bridges: A:R.546, A:R.546, A:R.578, A:K.583 pi-Stacking: A:F.591 GDP.20: 18 residues within 4Å: Chain B: S.543, R.546, H.547, Y.550, A.564, D.565, F.566, 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:H.547, B:Y.550, B:A.567, B:A.567, B:L.569, B:R.574, B:S.589, B:K.592 Salt bridges: B:R.546, B:R.546, B:H.547, B:R.578, B:K.583 pi-Stacking: B:F.591 GDP.32: 18 residues within 4Å: Chain C: S.543, R.546, H.547, Y.550, A.564, D.565, F.566, 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:Y.550, C:A.567, C:A.567, C:L.569, C:R.574, C:S.589, 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 NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.10: 1 residues within 4Å: Chain A: N.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.11: 3 residues within 4Å: Chain A: N.213, S.215, C.216 No protein-ligand interaction detected (PLIP) NAG.21: 1 residues within 4Å: Chain B: N.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.202 NAG.22: 3 residues within 4Å: Chain B: N.213, S.215, C.216 No protein-ligand interaction detected (PLIP) NAG.33: 1 residues within 4Å: Chain C: N.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.202 NAG.34: 3 residues within 4Å: Chain C: N.213, S.215, C.216 No protein-ligand interaction detected (PLIP)

3 x Q3G: O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine(Non-covalent)

Q3G.12: 12 residues within 4Å: Chain A: F.38, V.41, S.42, I.337, T.340, L.341, F.344, T.348 Chain B: S.342, Y.343, L.346, V.349 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.38, A:V.41, A:L.341, A:L.341, A:L.341, B:L.346 Hydrogen bonds: A:T.348 Q3G.23: 12 residues within 4Å: Chain B: F.38, V.41, S.42, I.337, T.340, L.341, F.344, T.348 Chain C: S.342, Y.343, L.346, V.349 8 PLIP interactions: 1 interactions with chain C, 7 interactions with chain B Hydrophobic interactions: C:L.346, B:F.38, B:V.41, B:I.337, B:L.341, B:L.341, B:L.341 Hydrogen bonds: B:T.348 Q3G.35: 12 residues within 4Å: Chain A: S.342, Y.343, L.346, V.349 Chain C: F.38, V.41, S.42, I.337, T.340, L.341, F.344, T.348 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.38, C:V.41, C:L.341, C:L.341, A:L.346 Hydrogen bonds: C:T.348

12 x PLM: PALMITIC ACID(Covalent)

PLM.13: 7 residues within 4Å: Chain A: L.353, N.356, T.357, S.360 Chain C: I.337 Ligands: PLM.14, PLM.15 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.353 PLM.14: 6 residues within 4Å: Chain A: T.357, S.360, C.362, C.363 Ligands: PLM.13, PLM.15 No protein-ligand interaction detected (PLIP) PLM.15: 10 residues within 4Å: Chain A: L.353, I.354, T.357, Y.358, C.363, V.367, Y.368 Ligands: PLM.13, PLM.14, PLM.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.353, A:I.354, A:Y.358, A:Y.358 PLM.16: 5 residues within 4Å: Chain A: Y.358, Y.368, C.371, C.374 Ligands: PLM.15 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.358 PLM.24: 7 residues within 4Å: Chain A: I.337 Chain B: L.353, N.356, T.357, S.360 Ligands: PLM.25, PLM.26 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.353 PLM.25: 6 residues within 4Å: Chain B: T.357, S.360, C.362, C.363 Ligands: PLM.24, PLM.26 No protein-ligand interaction detected (PLIP) PLM.26: 10 residues within 4Å: Chain B: L.353, I.354, T.357, Y.358, C.363, V.367, Y.368 Ligands: PLM.24, PLM.25, PLM.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.353 PLM.27: 5 residues within 4Å: Chain B: Y.358, Y.368, C.371, C.374 Ligands: PLM.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.358 PLM.36: 7 residues within 4Å: Chain B: I.337 Chain C: L.353, N.356, T.357, S.360 Ligands: PLM.37, PLM.38 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.353 PLM.37: 6 residues within 4Å: Chain C: T.357, C.362, C.363, V.367 Ligands: PLM.36, PLM.38 No protein-ligand interaction detected (PLIP) PLM.38: 10 residues within 4Å: Chain C: L.353, I.354, T.357, Y.358, C.363, V.367, Y.368 Ligands: PLM.36, PLM.37, PLM.39 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.353, C:I.354, C:Y.358 PLM.39: 5 residues within 4Å: Chain C: Y.358, Y.368, C.371, C.374 Ligands: PLM.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.358

3 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.17: 16 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: P.142, Q.143, F.288, P.289, N.292, R.294, K.311 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:K.64, A:K.66, A:T.189, B:Q.143, B:N.292 Salt bridges: A:K.64, A:K.64, A:K.66, A:K.193, B:R.294, B:K.311, B:K.311 pi-Cation interactions: A:K.66 ATP.28: 15 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: P.142, Q.143, F.288, N.292, R.294, K.311 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:K.64, B:K.66, B:T.189, C:N.292 Salt bridges: B:K.64, B:K.66, B:K.193, C:R.294, C:K.311, C:K.311 pi-Cation interactions: B:K.66 ATP.29: 16 residues within 4Å: Chain A: P.142, Q.143, 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 12 PLIP interactions: 6 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:Q.143, A:N.292, C:K.64, C:T.189 Salt bridges: A:K.145, A:R.294, A:K.311, A:K.311, C:K.64, C:K.66, C:K.193 pi-Cation interactions: C:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

McCarthy, A.E. et al., Full-Length P2X7Structures Reveal How Palmitoylation Prevents Channel Desensitization. Cell (2019)

Release Date

2019-10-23

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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