SMTL ID : 4dw0.1

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 2.9 Angstroms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-trimer

Ligands

3 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 4 residues within 4Å: Chain A: N.188, Y.191, T.201, D.202 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.201 Hydrophobic interactions: A:Y.191 NAG-NAG-BMA-MAN.8: 4 residues within 4Å: Chain B: N.188, Y.191, T.201, D.202 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.201 Hydrophobic interactions: B:Y.191 NAG-NAG-BMA-MAN.15: 4 residues within 4Å: Chain C: N.188, Y.191, T.201, D.202 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.201 Hydrophobic interactions: C:Y.191

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

NAG.2: 2 residues within 4Å: Chain A: N.88 Chain C: G.283 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.88 NAG.9: 2 residues within 4Å: Chain A: G.283 Chain B: N.88 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.88 NAG.16: 2 residues within 4Å: Chain B: G.283 Chain C: N.88 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.88

3 x GD: GADOLINIUM ATOM(Non-covalent)

GD.3: 1 residues within 4Å: Chain A: E.161 No protein-ligand interaction detected (PLIP) GD.10: 1 residues within 4Å: Chain B: E.161 No protein-ligand interaction detected (PLIP) GD.17: 1 residues within 4Å: Chain C: E.161 No protein-ligand interaction detected (PLIP)

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 8 residues within 4Å: Chain A: S.41, V.42, T.43, K.168, N.170 Chain C: L.257, D.258, R.296 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:S.41, A:T.43, A:N.170, A:N.170, A:N.170, C:R.296 Water bridges: A:K.168, A:K.168 GOL.5: 7 residues within 4Å: Chain A: K.47, G.48, D.63, V.64 Chain C: R.118, G.119 Ligands: GOL.6 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.48, A:G.48, A:V.64 Water bridges: A:D.63, C:R.273 GOL.6: 9 residues within 4Å: Chain A: G.48, I.49, R.162, F.163, T.164, R.209 Chain C: N.115, G.119 Ligands: GOL.5 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:I.49, A:R.162, A:T.164, A:R.209, C:N.115 GOL.7: 9 residues within 4Å: Chain A: V.42, T.44, Q.72, E.73, D.74, G.75, S.76 Chain C: Y.270, R.296 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:T.44, A:D.74, A:G.75, C:Y.270, C:Y.270 Water bridges: A:V.42, A:T.44, A:E.73 GOL.11: 8 residues within 4Å: Chain A: L.257, D.258, R.296 Chain B: S.41, V.42, T.43, K.168, N.170 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.41, B:T.43, B:N.170, B:N.170, B:N.170, A:R.296 Water bridges: B:K.168, B:K.168 GOL.12: 7 residues within 4Å: Chain A: R.118, G.119 Chain B: K.47, G.48, D.63, V.64 Ligands: GOL.13 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.48, B:G.48, B:V.64 Water bridges: B:D.63, A:R.273 GOL.13: 9 residues within 4Å: Chain A: N.115, G.119 Chain B: G.48, I.49, R.162, F.163, T.164, R.209 Ligands: GOL.12 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.49, B:R.162, B:T.164, B:R.209, A:N.115 GOL.14: 9 residues within 4Å: Chain A: Y.270, R.296 Chain B: V.42, T.44, Q.72, E.73, D.74, G.75, S.76 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.44, B:D.74, B:G.75, A:Y.270, A:Y.270 Water bridges: B:V.42, B:T.44, B:E.73 GOL.18: 8 residues within 4Å: Chain B: L.257, D.258, R.296 Chain C: S.41, V.42, T.43, K.168, N.170 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:S.41, C:T.43, C:N.170, C:N.170, C:N.170, B:R.296 Water bridges: C:K.168, C:K.168 GOL.19: 7 residues within 4Å: Chain B: R.118, G.119 Chain C: K.47, G.48, D.63, V.64 Ligands: GOL.20 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.48, C:G.48, C:V.64 Water bridges: C:D.63, B:R.273 GOL.20: 9 residues within 4Å: Chain B: N.115, G.119 Chain C: G.48, I.49, R.162, F.163, T.164, R.209 Ligands: GOL.19 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:I.49, C:R.162, C:T.164, C:R.209, B:N.115 GOL.21: 9 residues within 4Å: Chain B: Y.270, R.296 Chain C: V.42, T.44, Q.72, E.73, D.74, G.75, S.76 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:Y.270, B:Y.270, C:T.44, C:D.74, C:G.75 Water bridges: C:V.42, C:T.44, C:E.73

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