SMTL ID : 3h9v.1

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.1 Angstroms

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

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: 4 residues within 4Å: Chain A: N.88, T.90, C.143, P.144 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: N.188, Y.191, D.202 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.191 NAG-NAG.5: 4 residues within 4Å: Chain B: N.88, T.90, C.143, P.144 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: N.188, Y.191, D.202 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.191 NAG-NAG.9: 4 residues within 4Å: Chain C: N.88, T.90, C.143, P.144 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain C: N.188, Y.191, D.202 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.191

6 x GD: GADOLINIUM ATOM(Non-covalent)

GD.3: 2 residues within 4Å: Chain A: E.161, Q.222 No protein-ligand interaction detected (PLIP) GD.4: 8 residues within 4Å: Chain A: E.73, D.74 Chain B: E.73, D.74 Chain C: E.73, D.74 Ligands: GD.8, GD.12 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Metal complexes: C:E.73, C:D.74, B:D.74, A:E.73, A:D.74 GD.7: 2 residues within 4Å: Chain B: E.161, Q.222 No protein-ligand interaction detected (PLIP) GD.8: 8 residues within 4Å: Chain A: E.73, D.74 Chain B: E.73, D.74 Chain C: E.73, D.74 Ligands: GD.4, GD.12 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Metal complexes: C:E.73, C:D.74, B:D.74, A:E.73, A:D.74 GD.11: 2 residues within 4Å: Chain C: E.161, Q.222 No protein-ligand interaction detected (PLIP) GD.12: 8 residues within 4Å: Chain A: E.73, D.74 Chain B: E.73, D.74 Chain C: E.73, D.74 Ligands: GD.4, GD.8 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 interactions with chain A Metal complexes: C:E.73, C:D.74, B:D.74, A:E.73, A:D.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawate, T. et al., Crystal structure of the ATP-gated P2X(4) ion channel in the closed state. Nature (2009)

Release Date

2009-07-28

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