SMTL ID : 4dw1.1

Crystal structure of the ATP-gated P2X4 ion channel in the ATP-bound, open state at 2.8 Angstroms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.1: 7 residues within 4Å: Chain A: N.186, I.187, N.188, Y.191, H.194, T.201, D.202 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.191 NAG-NAG-BMA-MAN-MAN-MAN.6: 7 residues within 4Å: Chain B: N.186, I.187, N.188, Y.191, H.194, T.201, D.202 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.191 NAG-NAG-BMA-MAN-MAN-MAN.11: 7 residues within 4Å: Chain C: N.186, I.187, N.188, Y.191, H.194, T.201, D.202 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.191

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

NAG.2: 1 residues within 4Å: Chain A: N.88 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.88 Hydrogen bonds: A:N.88 NAG.7: 1 residues within 4Å: Chain B: N.88 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.88 Hydrogen bonds: B:N.88 NAG.12: 1 residues within 4Å: Chain C: N.88 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:N.88 Hydrogen bonds: C:N.88

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

ATP.3: 15 residues within 4Å: Chain A: R.118, A.267, N.271, R.273, K.291 Chain C: K.45, V.46, K.47, T.164, V.165, L.166, L.192, I.207 Ligands: GOL.4, GOL.5 13 PLIP interactions: 8 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:T.164, C:T.164, C:L.166, A:N.271 Salt bridges: C:K.45, C:K.45, C:K.45, C:K.47, A:R.273, A:K.291, A:K.291 pi-Cation interactions: C:K.47 Water bridges: A:K.291 ATP.8: 15 residues within 4Å: Chain A: K.45, V.46, K.47, T.164, V.165, L.166, L.192, I.207 Chain B: R.118, A.267, N.271, R.273, K.291 Ligands: GOL.9, GOL.10 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:T.164, A:T.164, A:L.166, B:N.271 Salt bridges: A:K.45, A:K.45, A:K.45, A:K.47, B:R.273, B:K.291, B:K.291 pi-Cation interactions: A:K.47 Water bridges: B:K.291 ATP.13: 15 residues within 4Å: Chain B: K.45, V.46, K.47, T.164, V.165, L.166, L.192, I.207 Chain C: R.118, A.267, N.271, R.273, K.291 Ligands: GOL.14, GOL.15 13 PLIP interactions: 5 interactions with chain C, 8 interactions with chain B Hydrogen bonds: C:N.271, B:T.164, B:T.164, B:L.166 Water bridges: C:K.291 Salt bridges: C:R.273, C:K.291, C:K.291, B:K.45, B:K.45, B:K.45, B:K.47 pi-Cation interactions: B:K.47

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: P.268, G.269, Y.270, N.271 Chain C: T.43, K.45, L.166, K.168 Ligands: ATP.3 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:P.268, A:N.271, C:T.43, C:T.43, C:K.168 GOL.5: 2 residues within 4Å: Chain A: K.291 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.291 GOL.9: 9 residues within 4Å: Chain A: T.43, K.45, L.166, K.168 Chain B: P.268, G.269, Y.270, N.271 Ligands: ATP.8 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:P.268, B:N.271, A:T.43, A:T.43, A:K.168 GOL.10: 2 residues within 4Å: Chain B: K.291 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.291 GOL.14: 9 residues within 4Å: Chain B: T.43, K.45, L.166, K.168 Chain C: P.268, G.269, Y.270, N.271 Ligands: ATP.13 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:P.268, C:N.271, B:T.43, B:T.43, B:K.168 GOL.15: 2 residues within 4Å: Chain C: K.291 Ligands: ATP.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hattori, M. et al., Molecular mechanism of ATP binding and ion channel activation in P2X receptors. Nature (2012)

Release Date

2012-04-25

Peptides

P2X purinoceptor: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Membrane

We predict this structure to be a membrane protein.
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P2X purinoceptor

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