5A2F Cell Adhesion date May 18, 2015
title Two Membrane Distal Igsf Domains Of Cd166
authors P.E.Chappell, S.Johnson, S.M.Lea, M.H.Brown
compound source
Molecule: Cd166 Antigen
Chain: A
Fragment: Two Membrane Distal Igsf Domains
Synonym: Activated Leukocyte Cell Adhesion Molecule, Human
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Cho Lec 3.2.8.1
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_vector_type: Plasmid
Expression_system_vector: Pee14
symmetry Space Group: P 43 21 2
R_factor 0.222 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.320 72.320 105.040 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.86 Å
ligand EDO, NAG enzyme
Primary referenceStructures of CD6 and Its Ligand CD166 Give Insight into Their Interaction., Chappell PE, Garner LI, Yan J, Metcalfe C, Hatherley D, Johnson S, Robinson CV, Lea SM, Brown MH, Structure. 2015 Jun 22. pii: S0969-2126(15)00222-1. doi:, 10.1016/j.str.2015.05.019. PMID:26146185
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (5a2f.pdb1.gz) 42 Kb
  • LPC: Ligand-Protein Contacts for 5A2F
  • CSU: Contacts of Structural Units for 5A2F
  • Structure Factors (426 Kb)
  • Retrieve 5A2F in mmCIF format [Save to disk]
  • Re-refined 5a2f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5A2F 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 5A2F
  • 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
  • Fold representative 5a2f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5a2f] [5a2f_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5A2F: [IG] [IG_like ] by SMART
  • Other resources with information on 5A2F
  • Community annotation for 5A2F at PDBWiki (http://pdbwiki.org)

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