2JA4 Immune System date Nov 21, 2006
title Crystal Structure Of Cd5 Domain III Reveals The Fold Of A Gr Scavenger Cysteine-Rich Receptor
authors B.Rodamilans, I.G.Munoz, M.R.Sarrias, F.Lozano, F.J.Blanco, G.Mon
compound source
Molecule: T-Cell Surface Glycoprotein Cd5
Chain: A
Fragment: Domain III, Residues 269-369
Synonym: Cd5diii, Lymphocyte Antigen T1leu-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell: B-Lymphocyte
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek-293ebna
Expression_system_tissue: Kidney Cells
Expression_system_plasmid: Pcep-Pu
symmetry Space Group: P 32 2 1
R_factor 0.193 R_Free 0.248
length a length b length c angle alpha angle beta angle gamma
62.931 62.931 72.564 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.21 Å

Primary referenceCrystal structure of the third extracellular domain of CD5 reveals the fold of a group B scavenger cysteine-rich receptor domain., Rodamilans B, Munoz IG, Bragado-Nilsson E, Sarrias MR, Padilla O, Blanco FJ, Lozano F, Montoya G, J Biol Chem. 2007 Apr 27;282(17):12669-77. Epub 2007 Feb 23. PMID:17322294
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (22 Kb) [Save to disk]
  • Biological Unit Coordinates (2ja4.pdb1.gz) 18 Kb
  • CSU: Contacts of Structural Units for 2JA4
  • Likely Quarternary Molecular Structure file(s) for 2JA4
  • Structure Factors (54 Kb)
  • Retrieve 2JA4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JA4 from S2C, [Save to disk]
  • Re-refined 2ja4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2JA4 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 2JA4
  • 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 2JA4, from MSDmotif at EBI
  • Fold representative 2ja4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ja4] [2ja4_A]
  • SWISS-PROT database: [P06127]
  • Domain organization of [CD5_HUMAN] by SWISSPFAM
  • Domain found in 2JA4: [SR ] by SMART
  • Other resources with information on 2JA4
  • Community annotation for 2JA4 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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