SMTL ID : 5wzy.1

Crystal structure of the P2X4 receptor from zebrafish in the presence of CTP 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 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP)

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

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

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: A.267, P.268, G.269, Y.270, N.271 Chain B: T.43, K.45, L.166, K.168 Ligands: CTP.5 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:P.268, A:N.271, B:K.168 Water bridges: A:N.271, B:T.44 GOL.4: 2 residues within 4Å: Chain A: K.291 Ligands: CTP.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.291 Water bridges: A:E.146 GOL.8: 10 residues within 4Å: Chain B: A.267, P.268, G.269, Y.270, N.271 Chain C: T.43, K.45, L.166, K.168 Ligands: CTP.10 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:K.168, B:P.268, B:N.271 Water bridges: C:T.44, B:N.271 GOL.9: 2 residues within 4Å: Chain B: K.291 Ligands: CTP.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.291 Water bridges: B:E.146 GOL.13: 10 residues within 4Å: Chain A: T.43, K.45, L.166, K.168 Chain C: A.267, P.268, G.269, Y.270, N.271 Ligands: CTP.15 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:P.268, C:N.271, A:K.168 Water bridges: C:N.271, A:T.44 GOL.14: 2 residues within 4Å: Chain C: K.291 Ligands: CTP.15 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.291 Water bridges: C:E.146

3 x CTP: CYTIDINE-5'-TRIPHOSPHATE(Non-covalent)

CTP.5: 14 residues within 4Å: Chain A: R.118, A.267, N.271, R.273, K.291 Chain B: K.45, K.47, T.164, V.165, L.166, L.192, I.207 Ligands: GOL.3, GOL.4 14 PLIP interactions: 6 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:R.118, A:N.271, B:T.164, B:T.164, B:L.166 Water bridges: A:K.291 Salt bridges: A:R.273, A:K.291, A:K.291, B:K.45, B:K.45, B:K.45, B:K.47 Hydrophobic interactions: B:L.166 CTP.10: 14 residues within 4Å: Chain B: R.118, A.267, N.271, R.273, K.291 Chain C: K.45, K.47, T.164, V.165, L.166, L.192, I.207 Ligands: GOL.8, GOL.9 14 PLIP interactions: 8 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.166 Hydrogen bonds: C:T.164, C:T.164, C:L.166, B:R.118, B:N.271 Salt bridges: C:K.45, C:K.45, C:K.45, C:K.47, B:R.273, B:K.291, B:K.291 Water bridges: B:K.291 CTP.15: 14 residues within 4Å: Chain A: K.45, 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.13, GOL.14 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain C Hydrophobic interactions: A:L.166 Hydrogen bonds: A:T.164, A:T.164, A:L.166, C:R.118, C:N.271 Salt bridges: A:K.45, A:K.45, A:K.45, A:K.47, C:R.273, C:K.291, C:K.291 Water bridges: C:K.291

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasuya, G. et al., Structural insights into the nucleotide base specificity of P2X receptors. Sci Rep (2017)

Release Date

2017-04-05

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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