SMTL ID : 6u9v.1

Cryo electron microscopy structure of the ATP-gated rat P2X7 ion channel in the apo, closed 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: 5 residues within 4Å: Chain A: P.179, R.183, N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.179, A:T.243 NAG-NAG.2: 5 residues within 4Å: Chain A: R.183, S.184, E.186, N.187, R.230 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain B: P.179, R.183, N.241, T.243, E.244, V.247 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.179, B:T.243 NAG-NAG.4: 5 residues within 4Å: Chain B: R.183, S.184, E.186, N.187, R.230 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: P.179, R.183, N.241, T.243, E.244 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:P.179, C:T.243 NAG-NAG.6: 5 residues within 4Å: Chain C: R.183, S.184, E.186, N.187, R.230 No protein-ligand interaction detected (PLIP)

3 x GLC- GLC: alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose(Non-covalent)

GLC-GLC.7: 13 residues within 4Å: Chain A: R.20, K.30, W.31, H.34 Chain B: V.349, L.353, N.356 Chain C: D.9, V.10, Q.12, E.14 Ligands: Q3G.16, PLM.34 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:D.9, B:N.356, A:R.20, A:K.30 GLC-GLC.8: 13 residues within 4Å: Chain A: D.9, V.10, Q.12, E.14 Chain B: R.20, K.30, W.31, H.34 Chain C: V.349, L.353, N.356 Ligands: Q3G.29, PLM.47 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: A:D.9, B:R.20, B:K.30, C:N.356 GLC-GLC.9: 13 residues within 4Å: Chain A: V.349, L.353, N.356 Chain B: D.9, V.10, Q.12, E.14 Chain C: R.20, K.30, W.31, H.34 Ligands: PLM.21, Q3G.42 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:N.356, B:D.9, C:R.20, C:K.30

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

GDP.10: 18 residues within 4Å: Chain A: R.546, H.547, Y.550, A.554, 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 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 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.23: 18 residues within 4Å: Chain B: R.546, H.547, Y.550, A.554, 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 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:S.543, B:Y.550, B:A.567, B:A.567, B:A.567, B:L.569, B:R.574, B:R.574, B:S.589 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.36: 18 residues within 4Å: Chain C: R.546, H.547, Y.550, A.554, 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 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 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.11: 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.12: 6 residues within 4Å: Chain A: C.477, Q.478, C.479, C.482, C.498, C.499 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.477, A:C.479, A:C.482, A:C.498 ZN.24: 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.25: 5 residues within 4Å: Chain B: C.477, Q.478, C.479, 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.37: 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.38: 6 residues within 4Å: Chain C: C.477, Q.478, C.479, C.482, C.498, C.499 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.13: 1 residues within 4Å: Chain A: N.202 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain A: N.213, S.215, C.216, N.223 No protein-ligand interaction detected (PLIP) NAG.15: 4 residues within 4Å: Chain A: N.284, E.285, S.286 Chain C: G.211 No protein-ligand interaction detected (PLIP) NAG.26: 1 residues within 4Å: Chain B: N.202 No protein-ligand interaction detected (PLIP) NAG.27: 4 residues within 4Å: Chain B: N.213, S.215, C.216, N.223 No protein-ligand interaction detected (PLIP) NAG.28: 4 residues within 4Å: Chain A: G.211 Chain B: N.284, E.285, S.286 No protein-ligand interaction detected (PLIP) NAG.39: 1 residues within 4Å: Chain C: N.202 No protein-ligand interaction detected (PLIP) NAG.40: 4 residues within 4Å: Chain C: N.213, S.215, C.216, N.223 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.223 NAG.41: 4 residues within 4Å: Chain B: G.211 Chain C: N.284, E.285, S.286 No protein-ligand interaction detected (PLIP)

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

Q3G.16: 17 residues within 4Å: Chain A: F.38, V.41, S.42, L.45, I.337, L.341, F.344, G.345, T.348 Chain B: S.342, Y.343, L.346, V.349 Chain C: N.16 Ligands: GLC-GLC.7, Q3G.29, Q3G.42 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.41, A:L.341, A:L.341, A:F.344, B:L.346, B:V.349 Hydrogen bonds: A:L.341 Q3G.29: 15 residues within 4Å: Chain B: F.38, V.41, I.337, L.341, F.344, G.345, T.348 Chain C: S.342, Y.343, G.345, L.346, V.349 Ligands: GLC-GLC.8, Q3G.16, Q3G.42 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:V.41, B:L.341, B:L.341, B:F.344, C:L.346, C:V.349 Hydrogen bonds: B:L.341 Q3G.42: 17 residues within 4Å: Chain A: S.342, Y.343, G.345, L.346, V.349 Chain B: N.16 Chain C: F.38, V.41, S.42, I.337, L.341, F.344, G.345, T.348 Ligands: GLC-GLC.9, Q3G.16, Q3G.29 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:L.346, A:V.349, C:V.41, C:L.341, C:L.341, C:F.344 Hydrogen bonds: C:L.341

18 x PLM: PALMITIC ACID(Covalent)

PLM.17: 9 residues within 4Å: Chain A: L.353, T.357, S.360, C.362, C.363 Chain B: C.4 Ligands: PLM.18, PLM.21, PLM.35 Ligand excluded by PLIP PLM.18: 9 residues within 4Å: Chain A: C.350, L.353, I.354, T.357, Y.358, C.363, V.367 Ligands: PLM.17, PLM.19 Ligand excluded by PLIP PLM.19: 5 residues within 4Å: Chain A: Y.358, V.367, C.371, C.374 Ligands: PLM.18 Ligand excluded by PLIP PLM.20: 10 residues within 4Å: Chain A: V.24, N.25, Y.26, T.28, I.29, I.354, Y.358, C.377, N.380 Chain C: F.11 Ligand excluded by PLIP PLM.21: 10 residues within 4Å: Chain A: L.353, N.356, T.357, S.360, C.362 Chain B: C.4 Ligands: GLC-GLC.9, GLC-GLC.9, PLM.17, PLM.35 Ligand excluded by PLIP PLM.22: 4 residues within 4Å: Chain A: C.4, C.5 Ligands: PLM.43, PLM.47 Ligand excluded by PLIP PLM.30: 9 residues within 4Å: Chain B: L.353, T.357, C.362, R.366, V.367 Chain C: C.4 Ligands: PLM.31, PLM.34, PLM.48 Ligand excluded by PLIP PLM.31: 9 residues within 4Å: Chain B: C.350, L.353, I.354, T.357, Y.358, C.363, V.367 Ligands: PLM.30, PLM.32 Ligand excluded by PLIP PLM.32: 5 residues within 4Å: Chain B: Y.358, V.367, C.371, C.374 Ligands: PLM.31 Ligand excluded by PLIP PLM.33: 10 residues within 4Å: Chain A: F.11 Chain B: V.24, N.25, Y.26, T.28, I.29, I.354, Y.358, C.377, N.380 Ligand excluded by PLIP PLM.34: 10 residues within 4Å: Chain B: L.353, N.356, T.357, S.360, C.362 Chain C: C.4 Ligands: GLC-GLC.7, GLC-GLC.7, PLM.30, PLM.48 Ligand excluded by PLIP PLM.35: 4 residues within 4Å: Chain B: C.4, C.5 Ligands: PLM.17, PLM.21 Ligand excluded by PLIP PLM.43: 10 residues within 4Å: Chain A: C.4 Chain C: L.353, T.357, C.362, C.363, R.366, V.367 Ligands: PLM.22, PLM.44, PLM.47 Ligand excluded by PLIP PLM.44: 9 residues within 4Å: Chain C: C.350, L.353, I.354, T.357, Y.358, C.363, V.367 Ligands: PLM.43, PLM.45 Ligand excluded by PLIP PLM.45: 5 residues within 4Å: Chain C: Y.358, V.367, C.371, C.374 Ligands: PLM.44 Ligand excluded by PLIP PLM.46: 10 residues within 4Å: Chain B: F.11 Chain C: V.24, N.25, Y.26, T.28, I.29, I.354, Y.358, C.377, N.380 Ligand excluded by PLIP PLM.47: 10 residues within 4Å: Chain A: C.4 Chain C: L.353, N.356, T.357, S.360, C.362 Ligands: GLC-GLC.8, GLC-GLC.8, PLM.22, PLM.43 Ligand excluded by PLIP PLM.48: 4 residues within 4Å: Chain C: C.4, C.5 Ligands: PLM.30, PLM.34 Ligand excluded by PLIP

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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