2D97 Hydrolase date Dec 09, 2005
title Structure Of Vil-Xylanase
authors H.Miyatake, T.Hasegawa, A.Yamano
compound source
Molecule: Endo-1,4-Beta-Xylanase 2
Chain: A
Synonym: Xylanase 2, 1,4- Beta-D-Xylan Xylanohydrolase 2
Ec: 3.2.1.8
 Organism_scientific: Hypocrea Jecorina
Organism_taxid: 51453
symmetry Space Group: P 1 21 1
R_factor 0.198 R_Free 0.228
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.347 38.585 57.162 90.00 110.31 90.00
method X-Ray Diffractionresolution 2.01 Å
ligand IYR, TYI enzyme Hydrolase E.C.3.2.1.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceNew methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL)., Miyatake H, Hasegawa T, Yamano A, Acta Crystallogr D Biol Crystallogr. 2006 Mar;62(Pt 3):280-9. Epub 2006, Feb 22. PMID:16510975
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (36 Kb) [Save to disk]
  • Biological Unit Coordinates (2d97.pdb1.gz) 33 Kb
  • LPC: Ligand-Protein Contacts for 2D97
  • CSU: Contacts of Structural Units for 2D97
  • Likely Quarternary Molecular Structure file(s) for 2D97
  • Structure Factors (82 Kb)
  • Retrieve 2D97 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D97 from S2C, [Save to disk]
  • Re-refined 2d97 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2D97 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 2D97
  • 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 2D97, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d97] [2d97_A]
  • SWISS-PROT database: [P36217]
  • Domain organization of [XYN2_TRIRE] by SWISSPFAM
    • Other resources with information on 2D97
  • Community annotation for 2D97 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science