3I5D Transport Protein date Jul 05, 2009
title Crystal Structure Of The Atp-Gated P2x4 Ion Channel In The C State At 3.5 Angstroms (R3)
authors T.Kawate, J.C.Michel, E.Gouaux
compound source
Molecule: P2x Purinoceptor
Chain: A, B, C
Fragment: Unp Residues 28-381
Engineered: Yes
Mutation: Yes
Organism_scientific: Danio Rerio
Organism_common: Leopard Danio,Zebra Danio,Zebra Fish
Organism_taxid: 7955
Gene: P2rx4a, P2x4.1
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Sf9
Expression_system_vector_type: Bacmid
Expression_system_plasmid: Pfastbac
symmetry Space Group: H 3
R_factor 0.276 R_Free 0.289
length a length b length c angle alpha angle beta angle gamma
234.910 234.910 138.433 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.46 Å
ligand NAG enzyme
A, C, B
  • purinergic nucleotide recept...
  • extracellularly ATP-gated ca...
  • excitatory postsynaptic pote...

  • Primary referenceCrystal structure of the ATP-gated P2X(4) ion channel in the closed state., Kawate T, Michel JC, Birdsong WT, Gouaux E, Nature. 2009 Jul 30;460(7255):592-8. PMID:19641588
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (159 Kb) [Save to disk]
  • Biological Unit Coordinates (3i5d.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 3I5D
  • CSU: Contacts of Structural Units for 3I5D
  • Structure Factors (612 Kb)
  • Retrieve 3I5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3I5D from S2C, [Save to disk]
  • Re-refined 3i5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3I5D in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3I5D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3I5D, from MSDmotif at EBI
  • Fold representative 3i5d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3i5d_A] [3i5d_C] [3i5d] [3i5d_B]
  • SWISS-PROT database: [Q6NYR1]
  • Domain organization of [Q6NYR1_DANRE] by SWISSPFAM
  • Other resources with information on 3I5D
  • Community annotation for 3I5D at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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