1DBG Lyase date Nov 02, 1999
title Crystal Structure Of Chondroitinase B
authors W.Huang, A.Matte, Y.Li, Y.S.Kim, R.J.Linhardt, H.Su, M.Cygler
compound source
Molecule: Chondroitinase B
Chain: A
 Organism_scientific: Pedobacter Heparinus
Organism_taxid: 984
symmetry Space Group: P 1 21 1
R_factor 0.180 R_Free 0.210
crystal
cell
length a length b length c angle alpha angle beta angle gamma
50.600 74.400 58.700 90.00 92.90 90.00
method X-Ray Diffractionresolution 1.70 Å
ligand BGC, G4D, GCU, MAN, MXY, RAM, XYP enzyme
related structures by homologous chain: 1DBO, 1OFL
Primary referenceCrystal structure of chondroitinase B from Flavobacterium heparinum and its complex with a disaccharide product at 1.7 A resolution., Huang W, Matte A, Li Y, Kim YS, Linhardt RJ, Su H, Cygler M, J Mol Biol 1999 Dec 17;294(5):1257-69. PMID:10600383
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1dbg.pdb1.gz) 85 Kb
  • LPC: Ligand-Protein Contacts for 1DBG
  • CSU: Contacts of Structural Units for 1DBG
  • Likely Quarternary Molecular Structure file(s) for 1DBG
  • Structure Factors (432 Kb)
  • Retrieve 1DBG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DBG from S2C, [Save to disk]
  • Re-refined 1dbg structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1DBG 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 1DBG
  • 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 1DBG, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dbga_, region A [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: [1dbg] [1dbg_A]
  • SWISS-PROT database: [Q46079]
  • Domain organization of [CSLB_PEDHD] by SWISSPFAM
    • Other resources with information on 1DBG
  • Community annotation for 1DBG 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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