3VZE Sugar Binding Protein date Oct 11, 2012
title Crystal Structure Of Human Pancreatic Secretory Protein Zg16 Alpha1,3-Mannobiose
authors M.Kanagawa, Y.Yamaguchi
compound source
Molecule: Zymogen Granule Membrane Protein 16
Chain: A
Fragment: Unp Residues 21-159
Synonym: Zymogen Granule Protein 16, Hzg16, Secretory Lecti
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Zg16
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: E. Coli Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcold-I(Mbp Fusion)
symmetry Space Group: P 21 21 2
R_factor 0.183 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.320 73.195 30.501 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CL, MAN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural Basis for Multiple Sugar Recognition of Jacalin-related Human ZG16p Lectin., Kanagawa M, Liu Y, Hanashima S, Ikeda A, Chai W, Nakano Y, Kojima-Aikawa K, Feizi T, Yamaguchi Y, J Biol Chem. 2014 Jun 13;289(24):16954-65. doi: 10.1074/jbc.M113.539114. Epub, 2014 Apr 30. PMID:24790092
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (3vze.pdb1.gz) 25 Kb
  • LPC: Ligand-Protein Contacts for 3VZE
  • CSU: Contacts of Structural Units for 3VZE
  • Structure Factors (80 Kb)
  • Retrieve 3VZE in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VZE from S2C, [Save to disk]
  • Re-refined 3vze structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3VZE 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 3VZE
  • 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 3VZE, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vze] [3vze_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3VZE: [Jacalin ] by SMART
  • Other resources with information on 3VZE
  • Community annotation for 3VZE at PDBWiki (http://pdbwiki.org)

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