3C9Z Sugar Binding Protein, Plant Protein date Feb 19, 2008
title Sambucus Nigra Agglutinin II (Sna-II), Tetragonal Crystal Fo
authors L.Maveyraud, V.Guillet, L.Mourey
compound source
Molecule: Agglutinin II
Chain: A
Synonym: Sna-II
 Organism_scientific: Sambucus Nigra
Organism_common: European Elder, Elderberry
Tissue: Bark
symmetry Space Group: I 41 2 2
R_factor 0.160 R_Free 0.200
crystal
cell
length a length b length c angle alpha angle beta angle gamma
126.124 126.124 76.039 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.35 Å
ligand ACT, FUC, NAG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for sugar recognition, including the Tn carcinoma antigen, by the lectin SNA-II from Sambucus nigra., Maveyraud L, Niwa H, Guillet V, Svergun DI, Konarev PV, Palmer RA, Peumans WJ, Rouge P, Van Damme EJ, Reynolds CD, Mourey L, Proteins. 2008 Sep 17. PMID:18798567
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (106 Kb) [Save to disk]
  • Biological Unit Coordinates (3c9z.pdb1.gz) 99 Kb
  • LPC: Ligand-Protein Contacts for 3C9Z
  • CSU: Contacts of Structural Units for 3C9Z
  • Likely Quarternary Molecular Structure file(s) for 3C9Z
  • Structure Factors (977 Kb)
  • Retrieve 3C9Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3C9Z from S2C, [Save to disk]
  • Re-refined 3c9z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3C9Z 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 3C9Z
  • 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 3C9Z, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3c9z] [3c9z_A]
  • SWISS-PROT database: [P33183]
  • Domain organization of [NIGB_SAMNI] by SWISSPFAM
  • Domain found in 3C9Z: [RICIN ] by SMART
    • Other resources with information on 3C9Z
  • Community annotation for 3C9Z 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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