5Y4J Isomerase date Aug 03, 2017
title Crystal Structure Of Glucose Isomerase In Complex With Xylit Inhibitor In One Metal Binding Mode
authors J.E.Bae, I.J.Kim, K.H.Nam
compound source
Molecule: Xylose Isomerase
Chain: A
Fragment: Unp Residues 3-386
Ec: 5.3.1.5
Engineered: Yes
Mutation: Yes
Organism_scientific: Streptomyces Rubiginosus
Organism_taxid: 1929
Gene: Xyla
Expression_system: Streptomyces Rubiginosus
Expression_system_taxid: 1929
symmetry Space Group: I 2 2 2
R_factor 0.155 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.614 99.416 102.019 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.40 Å
ligand MG, XYL enzyme Isomerase E.C.5.3.1.5 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode., Bae JE, Kim IJ, Nam KH, Biochem Biophys Res Commun. 2017 Nov 4;493(1):666-670. doi:, 10.1016/j.bbrc.2017.08.134. Epub 2017 Sep 1. PMID:28865958
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (5y4j.pdb1.gz) 285 Kb
  • LPC: Ligand-Protein Contacts for 5Y4J
  • CSU: Contacts of Structural Units for 5Y4J
  • Structure Factors (2515 Kb)
  • Retrieve 5Y4J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y4J from S2C, [Save to disk]
  • View 5Y4J 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 5Y4J
  • 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: [5y4j_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y4J
  • Community annotation for 5Y4J at PDBWiki (http://pdbwiki.org)

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