3D34 Immune System date May 09, 2008
title Structure Of The F-Spondin Domain Of Mindin
authors Y.Li, R.A.Mariuzza
compound source
Molecule: Spondin-2
Chain: A, B
Fragment: F-Spondin Domain, Unp Residues 27-249
Synonym: Mindin, Differentially Expressed In Cancerous And Cancerous Lung Cells 1, Dil-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Spon2, Dil1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.189 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.600 68.027 110.130 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand CA, NI enzyme
Primary referenceStructure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule., Li Y, Cao C, Jia W, Yu L, Mo M, Wang Q, Huang Y, Lim JM, Ishihara M, Wells L, Azadi P, Robinson H, He YW, Zhang L, Mariuzza RA, EMBO J. 2009 Feb 4;28(3):286-97. Epub 2009 Jan 15. PMID:19153605
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3d34.pdb1.gz) 73 Kb
  • LPC: Ligand-Protein Contacts for 3D34
  • CSU: Contacts of Structural Units for 3D34
  • Likely Quarternary Molecular Structure file(s) for 3D34
  • Structure Factors (1485 Kb)
  • Retrieve 3D34 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3D34 from S2C, [Save to disk]
  • Re-refined 3d34 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3D34 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 3D34
  • 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 3D34, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3d34_A] [3d34] [3d34_B]
  • SWISS-PROT database: [Q9BUD6]
  • Domain organization of [SPON2_HUMAN] by SWISSPFAM
  • Other resources with information on 3D34
  • Community annotation for 3D34 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science