4P8V Sugar Binding Protein date Apr 01, 2014
title The Crystal Structures Of Ykl-39 In The Presence Of Chitooligosaccharides (Glcnac2) Were Solved To Resolutions Angstrom
authors W.Suginta, A.Ranok, R.C.Robinson, J.Wongsantichon
compound source
Molecule: Chitinase-3-Like Protein 2
Chain: A
Synonym: Chondrocyte Protein 39,Ykl-39
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Chi3l2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet32a(+)
symmetry Space Group: P 41 21 2
R_factor 0.173 R_Free 0.204
length a length b length c angle alpha angle beta angle gamma
70.682 70.682 140.255 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.64 Å
ligand NAG, SO4 enzyme

Primary referenceStructural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39)., Ranok A, Wongsantichon J, Robinson RC, Suginta W, J Biol Chem. 2014 Dec 4. pii: jbc.M114.588905. PMID:25477513
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (4p8v.pdb1.gz) 72 Kb
  • LPC: Ligand-Protein Contacts for 4P8V
  • CSU: Contacts of Structural Units for 4P8V
  • Structure Factors (782 Kb)
  • Retrieve 4P8V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P8V from S2C, [Save to disk]
  • Re-refined 4p8v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P8V 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 4P8V
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4P8V, from MSDmotif at EBI
  • Fold representative 4p8v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p8v_A] [4p8v]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4P8V: [Glyco_18 ] by SMART
  • Other resources with information on 4P8V
  • Community annotation for 4P8V at PDBWiki (http://pdbwiki.org)

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