3AP9 Sugar Binding Protein date Oct 12, 2010
title Crystal Structure Of The Galectin-8 N-Terminal Carbohydrate Recognition Domain In Complex With Lacto-N-Fucopentaose III
authors T.Matsuzaka, H.Ideo, K.Yamashita, T.Nonaka
compound source
Molecule: Galectin-8
Chain: A
Fragment: N-Terminal Carbohydrate Recognition Domain
Synonym: Gal-8, Po66 Carbohydrate-Binding Protein, Po66-Cbp Carcinoma Tumor Antigen 1, Pcta-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lgals8
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-2
symmetry Space Group: P 21 21 21
R_factor 0.157 R_Free 0.178
crystal
cell
length a length b length c angle alpha angle beta angle gamma
46.419 49.952 70.207 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.33 Å
ligand BGC, CL, FUC, GAL, MPD, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceGalectin-8-N-domain recognition mechanism for sialylated and sulfated glycans., Ideo H, Matsuzaka T, Nonaka T, Seko A, Yamashita K, J Biol Chem. 2011 Apr 1;286(13):11346-55. Epub 2011 Feb 2. PMID:21288902
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (37 Kb) [Save to disk]
  • Biological Unit Coordinates (3ap9.pdb1.gz) 32 Kb
  • LPC: Ligand-Protein Contacts for 3AP9
  • CSU: Contacts of Structural Units for 3AP9
  • Structure Factors (1746 Kb)
  • Retrieve 3AP9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3AP9 from S2C, [Save to disk]
  • Re-refined 3ap9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3AP9 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 3AP9
  • 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 3AP9, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ap9] [3ap9_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3AP9: [GLECT] [Gal-bind_lectin ] by SMART
  • Other resources with information on 3AP9
  • Community annotation for 3AP9 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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