SMTL ID : 5svr.1

Crystal structure of the ATP-gated human P2X3 ion channel bound to competitive antagonist A-317491

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.13 Å

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: M.165, E.168, N.169 Chain C: P.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.169 NAG.2: 3 residues within 4Å: Chain A: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.289, A:S.291, A:S.291 NAG.6: 4 residues within 4Å: Chain A: P.127 Chain B: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.169 NAG.7: 3 residues within 4Å: Chain B: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.289, B:S.291, B:S.291 NAG.11: 4 residues within 4Å: Chain B: P.127 Chain C: M.165, E.168, N.169 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.169 NAG.12: 3 residues within 4Å: Chain C: M.287, N.289, S.291 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.289, C:S.291, C:S.291

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: D.157 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: D.157 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain C: D.157 No protein-ligand interaction detected (PLIP)

3 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.9, NA.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322 NA.9: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.4, NA.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322 NA.14: 5 residues within 4Å: Chain A: I.322 Chain B: I.322 Chain C: I.322 Ligands: NA.4, NA.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.322

3 x 71C: 5-{[(3-phenoxyphenyl)methyl][(1S)-1,2,3,4-tetrahydronaphthalen-1-yl]carbamoyl}benzene-1,2,4-tricarboxylic acid(Non-covalent)

71C.5: 13 residues within 4Å: Chain A: S.271, S.272, V.273, R.280 Chain B: K.62, K.64, T.171, F.173, L.190, M.199, K.200, P.213, I.214 14 PLIP interactions: 4 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:V.273, A:V.273, B:K.62, B:K.64, B:F.173, B:F.173, B:F.173, B:L.190, B:M.199, B:K.200, B:P.213 Hydrogen bonds: A:R.280 Salt bridges: A:R.280, B:K.62 71C.10: 13 residues within 4Å: Chain B: S.271, S.272, V.273, R.280 Chain C: K.62, K.64, T.171, F.173, L.190, M.199, K.200, P.213, I.214 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:K.62, C:K.64, C:F.173, C:F.173, C:F.173, C:L.190, C:M.199, C:K.200, C:P.213, B:V.273, B:V.273 Salt bridges: C:K.62, B:R.280 Hydrogen bonds: B:R.280 71C.15: 13 residues within 4Å: Chain A: K.62, K.64, T.171, F.173, L.190, M.199, K.200, P.213, I.214 Chain C: S.271, S.272, V.273, R.280 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:K.62, A:K.64, A:F.173, A:F.173, A:F.173, A:L.190, A:M.199, A:K.200, A:P.213, C:V.273, C:V.273 Salt bridges: A:K.62, C:R.280 Hydrogen bonds: C:R.280

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mansoor, S.E. et al., X-ray structures define human P2X3 receptor gating cycle and antagonist action. Nature (2016)

Release Date

2016-10-05

Peptides

P2X purinoceptor 3: 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 3

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