2WDB Hydrolase date Mar 23, 2009
title A Family 32 Carbohydrate-Binding Module, From The Mu Toxin P Clostridium Perfringens, In Complex With Beta-D-Glcnac-Beta Mannose
authors E.Ficko-Blean, A.B.Boraston
compound source
Molecule: Hyaluronoglucosaminidase
Chain: A, B, C, D
Fragment: Residues 807-975
Synonym: Hyaluronidase, Mu Toxin, Gh84a Cbm32-2
Ec: 3.2.1.35
Engineered: Yes
 Organism_scientific: Clostridium Perfringens
Organism_taxid: 1502
Atcc: 13124
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (Star) De3
Expression_system_plasmid: Pet28a
symmetry Space Group: P 31 2 1
R_factor 0.194 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.276 91.276 132.701 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.03 Å
ligand CA, MAN, NAG enzyme Hydrolase E.C.3.2.1.35 BRENDA
Primary referenceN-Acetylglucosamine Recognition by a Family 32 Carbohydrate-Binding Module from Clostridium perfringens NagH., Ficko-Blean E, Boraston AB, J Mol Biol. 2009 May 5. PMID:19422833
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (202 Kb) [Save to disk]
  • Biological Unit Coordinates (2wdb.pdb1.gz) 49 Kb
  • Biological Unit Coordinates (2wdb.pdb2.gz) 52 Kb
  • Biological Unit Coordinates (2wdb.pdb3.gz) 50 Kb
  • Biological Unit Coordinates (2wdb.pdb4.gz) 50 Kb
  • LPC: Ligand-Protein Contacts for 2WDB
  • CSU: Contacts of Structural Units for 2WDB
  • Likely Quarternary Molecular Structure file(s) for 2WDB
  • Structure Factors (309 Kb)
  • Retrieve 2WDB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2WDB from S2C, [Save to disk]
  • Re-refined 2wdb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2WDB 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 2WDB
  • 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 2WDB, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2wdb_C] [2wdb_B] [2wdb_D] [2wdb] [2wdb_A]
  • SWISS-PROT database: [P26831]
  • Domain organization of [NAGH_CLOPE] by SWISSPFAM
  • Domain found in 2WDB: [FA58C ] by SMART
    • Other resources with information on 2WDB
  • Community annotation for 2WDB 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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