1MD6 Immune System date Aug 07, 2002
title High Resolution Crystal Structure Of Murine Il-1f5 Reveals Unique Loop Conformation For Specificity
authors X.Y.Pei, E.F.Dunn, N.J.Gay, L.A.O'Neill
compound source
Molecule: Interleukin 1 Family, Member 5 (Delta)
Chain: A
Synonym: Il-1f5, Interleukin-1f5, Interleukin 1 Receptor Antagonist Homolog 1;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet21a
symmetry Space Group: P 32 2 1
R_factor 0.204 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
78.932 78.932 69.740 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.60 Å
Gene
Ontology
ChainFunctionProcessComponent
A
  • cytokine activity


  • Primary referenceHigh-resolution structure of murine interleukin 1 homologue IL-1F5 reveals unique loop conformations for receptor binding specificity., Dunn EF, Gay NJ, Bristow AF, Gearing DP, O'Neill LA, Pei XY, Biochemistry 2003 Sep 23;42(37):10938-44. PMID:12974628
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (32 Kb) [Save to disk]
  • Biological Unit Coordinates (1md6.pdb1.gz) 28 Kb
  • CSU: Contacts of Structural Units for 1MD6
  • Likely Quarternary Molecular Structure file(s) for 1MD6
  • Structure Factors (307 Kb)
  • Retrieve 1MD6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1MD6 from S2C, [Save to disk]
  • Re-refined 1md6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1MD6 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 1MD6
  • 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
  • 3D motif for 1MD6, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1md6a_, region A [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1md6] [1md6_A]
  • SWISS-PROT database: [Q9QYY1]
  • Domain organization of [IL1F5_MOUSE] by SWISSPFAM
  • Domain found in 1MD6: [IL1 ] by SMART
  • Other resources with information on 1MD6
  • Community annotation for 1MD6 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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