4DVO Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9 date
authors Kovalevsky, A.Y., Hanson, L., Langan, P.
compound source
symmetry
R_factor
R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.00
ligand NI, SOR enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography., Kovalevsky A, Hanson BL, Mason SA, Forsyth VT, Fisher Z, Mustyakimov M, Blakeley MP, Keen DA, Langan P, Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1201-6. Epub 2012 Aug 18. PMID:22948921
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (145 Kb) [Save to disk]
  • Biological Unit Coordinates (4dvo.pdb1.gz) 558 Kb
  • LPC: Ligand-Protein Contacts for 4DVO
  • CSU: Contacts of Structural Units for 4DVO
  • Structure Factors (1040 Kb)
  • Retrieve 4DVO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DVO from S2C, [Save to disk]
  • Re-refined 4dvo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4DVO 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 4DVO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4DVO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4dvo_A] [4dvo]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 4DVO
  • Community annotation for 4DVO at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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