4XYN X-ray structure of Ca(2+)-S100B with human RAGE-derived W61 peptide date
authors Jensen, J.L., Indurthi, V.S.K., Neau, D., Vetter, S.W., Colbert, C.L.
compound source
symmetry
R_factor
R_Free 0.2537
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.55
ligand CA enzyme
note 4XYN supersedes 4N6I
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructural insights into the binding of the human receptor for advanced glycation end products (RAGE) by S100B, as revealed by an S100B-RAGE-derived peptide complex., Jensen JL, Indurthi VS, Neau DB, Vetter SW, Colbert CL, Acta Crystallogr D Biol Crystallogr. 2015 May;71(Pt 5):1176-83. doi:, 10.1107/S1399004715004216. Epub 2015 Apr 25. PMID:25945582
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (123 Kb) [Save to disk]
  • Biological Unit Coordinates (4xyn.pdb1.gz) 62 Kb
  • Biological Unit Coordinates (4xyn.pdb2.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 4XYN
  • CSU: Contacts of Structural Units for 4XYN
  • Structure Factors (227 Kb)
  • Retrieve 4XYN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XYN from S2C, [Save to disk]
  • Re-refined 4xyn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XYN 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 4XYN
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4XYN, from MSDmotif at EBI
  • Fold representative 4xyn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xyn_P] [4xyn] [4xyn_A] [4xyn_D] [4xyn_B] [4xyn_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4XYN: [S_100 ] by SMART
  • Other resources with information on 4XYN
  • Community annotation for 4XYN at PDBWiki (http://pdbwiki.org)

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