5DG1 Sugar Binding Protein date Aug 27, 2015
title Sugar Binding Protein - Human Galectin-2
authors J.Y.Su, Y.L.Si
compound source
Molecule: Galectin-2
Chain: A, B, C, D, H, I
Synonym: Gal-2,Beta-Galactoside-Binding Lectin L-14-II,Hl14 Binding Lectin 2,S-Lac Lectin 2;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lgals2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 2 21 21
R_factor 0.297 R_Free 0.321
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.500 106.780 182.110 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.20 Å
ligand BGC, GAL enzyme
Gene
Ontology
ChainFunctionProcessComponent
H, A, D, C, I, B


Primary referenceHuman galectin-2 interacts with carbohydrates and peptides non-classically: new insight from X-ray crystallography and hemagglutination., Si Y, Feng S, Gao J, Wang Y, Zhang Z, Meng Y, Zhou Y, Tai G, Su J, Acta Biochim Biophys Sin (Shanghai). 2016 Aug 25. PMID:27563008
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (252 Kb) [Save to disk]
  • Biological Unit Coordinates (5dg1.pdb1.gz) 84 Kb
  • Biological Unit Coordinates (5dg1.pdb2.gz) 82 Kb
  • Biological Unit Coordinates (5dg1.pdb3.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 5DG1
  • CSU: Contacts of Structural Units for 5DG1
  • Structure Factors (236 Kb)
  • Retrieve 5DG1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DG1 from S2C, [Save to disk]
  • Re-refined 5dg1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5DG1 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 5DG1
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dg1_H] [5dg1_A] [5dg1_I] [5dg1_C] [5dg1_D] [5dg1] [5dg1_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5DG1: [GLECT] [Gal-bind_lectin ] by SMART
    • Other resources with information on 5DG1
  • Community annotation for 5DG1 at PDBWiki (http://pdbwiki.org)

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