2XYC Cell Adhesion date Nov 17, 2010
title Crystal Structure Of Ncam2 Igiv-Fn3i
authors N.Kulahin, K.K.Rasmussen, O.Kristensen, V.Berezin, E.Bock, P.S.Wa M.Gajhede
compound source
Molecule: Neural Cell Adhesion Molecule 2
Chain: A
Fragment: Igiv-F3i, Residues 301-591
Synonym: Ncam2
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Pichia Pastoris
Expression_system_taxid: 4922
symmetry Space Group: P 43 21 2
R_factor 0.194 R_Free 0.241
crystal
cell
length a length b length c angle alpha angle beta angle gamma
139.660 139.660 47.790 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand EPE, NAG, PO4 enzyme
note 2XYC supersedes 2JLK
Primary referenceStructural Model and trans-Interaction of the Entire Ectodomain of the Olfactory Cell Adhesion Molecule., Kulahin N, Kristensen O, Rasmussen KK, Olsen L, Rydberg P, Vestergaard B, Kastrup JS, Berezin V, Bock E, Walmod PS, Gajhede M, Structure. 2011 Feb 9;19(2):203-11. PMID:21300289
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (57 Kb) [Save to disk]
  • Biological Unit Coordinates (2xyc.pdb1.gz) 53 Kb
  • LPC: Ligand-Protein Contacts for 2XYC
  • CSU: Contacts of Structural Units for 2XYC
  • Structure Factors (124 Kb)
  • Retrieve 2XYC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XYC from S2C, [Save to disk]
  • Re-refined 2xyc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2XYC 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 2XYC
  • 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 2XYC, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xyc] [2xyc_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2XYC: [FN3] [IGc2 ] by SMART
    • Other resources with information on 2XYC
  • Community annotation for 2XYC 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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