SMTL ID : 9bqi.1

Cryo-EM structure of BAY-1797 bound to the full-length human P2X4 receptor in the 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: 2 residues within 4Å: Chain A: N.75, F.81 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.75, F.81 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain C: N.75, F.81 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: K.180, A.181, E.183, N.184 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.3: 9 residues within 4Å: Chain A: L.206, N.208, I.209, K.222, T.223, P.225, F.226, L.271, R.273 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.271 Hydrogen bonds: A:T.223, A:R.273, A:K.222 NAG-NAG-BMA.6: 9 residues within 4Å: Chain B: L.206, N.208, I.209, K.222, T.223, P.225, F.226, L.271, R.273 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.271 Hydrogen bonds: B:T.223, B:R.273, B:K.222 NAG-NAG-BMA.9: 9 residues within 4Å: Chain C: L.206, N.208, I.209, K.222, T.223, P.225, F.226, L.271, R.273 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.271 Hydrogen bonds: C:T.223, C:R.273, C:K.222

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

NAG.10: 1 residues within 4Å: Chain A: N.199 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.199 NAG.16: 1 residues within 4Å: Chain B: N.199 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.199 NAG.21: 1 residues within 4Å: Chain C: N.199 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.199

3 x P6E: N-[4-(3-chloranylphenoxy)-3-sulfamoyl-phenyl]-2-phenyl-ethanamide(Non-covalent)

P6E.11: 25 residues within 4Å: Chain A: L.79, R.82, W.84, A.87, D.88, Y.89, V.90, I.91, P.92, A.93, M.102, V.105, L.107, F.294, F.296, K.298, I.312 Chain B: P.92, A.93, Q.94 Chain C: F.296, A.297, Y.299 Ligands: P6E.15, P6E.20 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:W.84, A:I.91, A:V.105, A:L.107, A:F.296, A:I.312 Hydrogen bonds: A:A.87, A:D.88, A:A.93, A:K.298, C:A.297 pi-Stacking: A:W.84 P6E.15: 25 residues within 4Å: Chain A: F.296, A.297, Y.299 Chain B: L.79, R.82, W.84, A.87, D.88, Y.89, V.90, I.91, P.92, A.93, M.102, V.105, L.107, F.294, F.296, K.298, I.312 Chain C: P.92, A.93, Q.94 Ligands: P6E.11, P6E.20 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.84, B:I.91, B:V.105, B:L.107, B:F.296, B:I.312 Hydrogen bonds: B:A.87, B:D.88, B:A.93, B:K.298, A:A.297 pi-Stacking: B:W.84 P6E.20: 25 residues within 4Å: Chain A: P.92, A.93, Q.94 Chain B: F.296, A.297, Y.299 Chain C: L.79, R.82, W.84, A.87, D.88, Y.89, V.90, I.91, P.92, A.93, M.102, V.105, L.107, F.294, F.296, K.298, I.312 Ligands: P6E.11, P6E.15 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.84, C:I.91, C:V.105, C:L.107, C:F.296, C:I.312 Hydrogen bonds: C:A.87, C:D.88, C:A.93, C:K.298, B:A.297 pi-Stacking: C:W.84

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.12: 21 residues within 4Å: Chain A: G.347, T.350, V.351 Chain B: P.18, I.20, L.30, N.32, R.33, A.34, Q.36, L.37, L.40, L.343, L.346 Chain C: F.11, L.12, D.16, P.18 Ligands: LMT.13, LMT.17, LMT.19 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:R.33, B:L.40, C:F.11, C:L.12 Hydrogen bonds: B:Q.36 LMT.13: 22 residues within 4Å: Chain A: V.351, I.355, L.358, Y.359, R.368, Y.372 Chain B: L.22, R.33, L.40, V.43, F.48, N.338, I.339, G.342, L.343, L.346 Chain C: A.10, F.11, E.14, Y.15, D.16 Ligands: LMT.12 13 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:Y.359, A:R.368, A:Y.372, A:Y.372, B:R.33, B:R.33, C:E.14, C:D.16 Hydrophobic interactions: B:V.43, B:F.48, B:I.339, B:L.343, B:L.343 LMT.14: 23 residues within 4Å: Chain A: A.10, F.11, E.14, Y.15, D.16 Chain B: V.351, I.355, L.358, Y.359, R.368, Y.372 Chain C: L.22, R.33, L.40, V.43, I.44, F.48, N.338, I.339, G.342, L.343, L.346 Ligands: LMT.17 13 PLIP interactions: 7 interactions with chain C, 2 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: C:V.43, C:F.48, C:I.339, C:L.343, C:L.343 Hydrogen bonds: C:R.33, C:R.33, A:E.14, A:D.16, B:Y.359, B:R.368, B:Y.372, B:Y.372 LMT.17: 21 residues within 4Å: Chain A: F.11, L.12, D.16, P.18 Chain B: G.347, T.350, V.351 Chain C: P.18, I.20, L.30, N.32, R.33, A.34, Q.36, L.37, L.40, L.343, L.346 Ligands: LMT.12, LMT.14, LMT.19 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:R.33, C:L.40, A:F.11, A:L.12 Hydrogen bonds: C:Q.36 LMT.18: 22 residues within 4Å: Chain A: L.22, R.33, L.40, V.43, F.48, N.338, I.339, G.342, L.343, L.346 Chain B: A.10, F.11, E.14, Y.15, D.16 Chain C: V.351, I.355, L.358, Y.359, R.368, Y.372 Ligands: LMT.19 13 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C, 7 interactions with chain A Hydrogen bonds: B:E.14, B:D.16, C:Y.359, C:R.368, C:Y.372, C:Y.372, A:R.33, A:R.33 Hydrophobic interactions: A:V.43, A:F.48, A:I.339, A:L.343, A:L.343 LMT.19: 21 residues within 4Å: Chain A: P.18, I.20, L.30, N.32, R.33, A.34, Q.36, L.37, L.40, L.343, L.346 Chain B: F.11, L.12, D.16, P.18 Chain C: G.347, T.350, V.351 Ligands: LMT.12, LMT.17, LMT.18 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.33, A:L.40, B:F.11, B:L.12 Hydrogen bonds: A:Q.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shi, H. et al., Human P2X4 receptor gating is modulated by a stable cytoplasmic cap and a unique allosteric pocket. Sci Adv (2025)

Release Date

2025-01-29

Peptides

P2X purinoceptor 4: 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 4

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