3BIB Immune System date Nov 30, 2007
title Tim-4 In Complex With Phosphatidylserine
authors C.Santiago, A.Ballesteros, G.G.Kaplan, G.J.Freeman, J.M.Casasnovas
compound source
Molecule: T-Cell Immunoglobulin And Mucin Domain- Containing Protein 4;
Chain: X
Fragment: N-Terminal Cys-Rich Domain
Synonym: Timd-4, T-Cell Membrane Protein 4, Tim-4, Spleen, Mucin- Containing, Knockout Of Lymphotoxin Protein, Smuckler;
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: Knowles Solter, C57bl6j
Gene: Timd4, Tim4
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet27b(+)
symmetry Space Group: P 63 2 2
R_factor 0.219 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.260 66.260 139.390 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.50 Å
ligand NA, PSF enzyme
Primary referenceStructures of T Cell Immunoglobulin Mucin Protein 4 Show a Metal-Ion-Dependent Ligand Binding Site where Phosphatidylserine Binds., Santiago C, Ballesteros A, Martinez-Munoz L, Mellado M, Kaplan GG, Freeman GJ, Casasnovas JM, Immunity. 2007 Dec;27(6):941-51. PMID:18083575
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (42 Kb) [Save to disk]
  • Biological Unit Coordinates (3bib.pdb1.gz) 38 Kb
  • LPC: Ligand-Protein Contacts for 3BIB
  • CSU: Contacts of Structural Units for 3BIB
  • Likely Quarternary Molecular Structure file(s) for 3BIB
  • Structure Factors (348 Kb)
  • Retrieve 3BIB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BIB from S2C, [Save to disk]
  • Re-refined 3bib structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BIB 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 3BIB
  • 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 3BIB, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bib] [3bib_X]
  • SWISS-PROT database: [Q6U7R4]
  • Domain organization of [TIMD4_MOUSE] by SWISSPFAM
  • Domain found in 3BIB: [IG ] by SMART
  • Other resources with information on 3BIB
  • Community annotation for 3BIB 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