3I5D

Crystal structure of the ATP-gated P2X4 ion channel in the closed, apo state at 3.5 Angstroms (R3)

Structural Biology Knowledgebase: 3I5D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.276

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3I5D

Classification: TRANSPORT PROTEIN

Total Structure Weight: 123646.50

Macromolecule Entities
Molecule Chains Length Organism Details
P2X purinoceptor A, B, C 356 Danio rerio Fragment: UNP residues 28-381
Mutation: H252R
Gene Name(s): p2rx4a

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Channels: Other Ion Channels

Protein Name: ATP-gated P2X4 ion channel (apo protein; ΔP2X4-B construct)


Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B, C N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.46 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.276
  • Space Group: H 3
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 234.91 α = 90.00
b = 234.91 β = 90.00
c = 138.43 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-05
  • Released Date: 2009-08-04
  • Deposition author(s): Kawate, T., Michel, J.C., Gouaux, E.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update