2XBD Hydrolase date Oct 27, 1998
title Internal Xylan Binding Domain From Cellulomonas Fimi Xylanas Minimized Average Structure
authors P.J.Simpson, D.N.Bolam, A.Cooper, A.Ciruela, G.P.Hazlewood, H.J.G M.P.Williamson
compound source
Molecule: Xylanase D
Chain: A
Fragment: Xylan Binding Domain 1
Synonym: Xbd1, Endo-1,4-Beta-Xylanase D
Ec: 3.2.1.8
Engineered: Yes
 Organism_scientific: Cellulomonas Fimi
Organism_taxid: 1708
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Jm83
methodSolution NMR
ligand
enzyme Hydrolase E.C.3.2.1.8 BRENDA
related structures by homologous chain: 1E5B
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity., Simpson PJ, Bolam DN, Cooper A, Ciruela A, Hazlewood GP, Gilbert HJ, Williamson MP, Structure Fold Des 1999 Jul 15;7(7):853-64. PMID:10425686
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (25 Kb) [Save to disk]
  • Biological Unit Coordinates (2xbd.pdb1.gz) 22 Kb
  • CSU: Contacts of Structural Units for 2XBD
  • Original NMR restraints for 2XBD from PDB
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 2XBD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XBD from S2C, [Save to disk]
    • View 2XBD 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 2XBD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2XBD, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2xbd__, region [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xbd] [2xbd_A]
  • SWISS-PROT database: [P54865]
  • Domain organization of [XYND_CELFI] by SWISSPFAM
  • Domain found in 2XBD: [CBD_II ] by SMART
    • Other resources with information on 2XBD
  • Community annotation for 2XBD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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