3VA2 Cytokine Cytokine Receptor date Dec 28, 2011
title Crystal Structure Of Human Interleukin-5 In Complex With Its Receptor
authors S.Kusano, M.Kukimoto-Niino, M.Shirouzu, S.Yokoyama
compound source
Molecule: Interleukin-5
Chain: A, B
Fragment: Unp Residues 23-134
Synonym: Il-5, B-Cell Differentiation Factor I, Eosinophil Differentiation Factor, T-Cell Replacing Factor, Trf;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il5
Expression_system: Cell-Free Synthesis

Molecule: Interleukin-5 Receptor Subunit Alpha
Chain: C
Fragment: Ectodomain, Unp Residues 21-335
Synonym: Il-5 Receptor Subunit Alpha, Il-5r Subunit Alpha, Alpha, Il-5ra, Cdw125;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Il5ra, Il5r
Expression_system: Cell-Free Synthesis
symmetry Space Group: P 21 21 21
R_factor 0.223 R_Free 0.276
length a length b length c angle alpha angle beta angle gamma
58.633 88.680 126.674 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
A, B


Primary referenceStructural basis of interleukin-5 dimer recognition by its alpha receptor., Kusano S, Kukimoto-Niino M, Hino N, Ohsawa N, Ikutani M, Takaki S, Sakamoto K, Hara-Yokoyama M, Shirouzu M, Takatsu K, Yokoyama S, Protein Sci. 2012 Jun;21(6):850-64. doi: 10.1002/pro.2072. Epub 2012 Apr 23. PMID:22528658
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (3va2.pdb1.gz) 184 Kb
  • CSU: Contacts of Structural Units for 3VA2
  • Structure Factors (234 Kb)
  • Retrieve 3VA2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VA2 from S2C, [Save to disk]
  • Re-refined 3va2 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VA2 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 3VA2
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3VA2, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v3va2, region A:113-294 [Jmol] [rasmolscript] [script source]
        - Domain d1q3va2, region A:130-341 [Jmol] [rasmolscript] [script source]
        - Domain d1u3va2, region A:163-338 [Jmol] [rasmolscript] [script source]
        - Domain d1j3va2, region A:2-157 [Jmol] [rasmolscript] [script source]
        - Domain d1m3va2, region A:33-71 [Jmol] [rasmolscript] [script source]
        - Domain d1h3va2, region A:342-445 [Jmol] [rasmolscript] [script source]
        - Domain d1l3va2, region A:469-876 [Jmol] [rasmolscript] [script source]
        - Domain d1c3va2, region A:606-714 [Jmol] [rasmolscript] [script source]
  • Fold representative 3va2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3va2_C] [3va2_A] [3va2] [3va2_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3VA2
  • Community annotation for 3VA2 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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