2VO5 Hydrolase date Feb 08, 2008
title Structural And Biochemical Evidence For A Boat-Like Transiti In Beta-Mannosidases
authors L.E.Tailford, W.A.Offen, N.L.Smith, C.Dumon, C.Moreland, J.Gratie M.P.Heck, R.V.Stick, Y.Bleriot, A.Vasella, H.J.Gilbert, G.J.Davi
compound source
Molecule: Beta-Mannosidase
Chain: A, B
Fragment: Residues 26-864
Ec: 3.2.1.25
Engineered: Yes
Organism_scientific: Bacteroides Thetaiotaomicron
Organism_taxid: 226186
Strain: Vpi-5482
Atcc: 29148
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pet28a
symmetry Space Group: P 1 21 1
R_factor 0.169 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
91.118 115.692 99.643 90.00 113.17 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand BR, CL, EDO, VBZ BindingDB enzyme Hydrolase E.C.3.2.1.25 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural and biochemical evidence for a boat-like transition state in beta-mannosidases., Tailford LE, Offen WA, Smith NL, Dumon C, Morland C, Gratien J, Heck MP, Stick RV, Bleriot Y, Vasella A, Gilbert HJ, Davies GJ, Nat Chem Biol. 2008 May;4(5):306-12. PMID:18408714
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (298 Kb) [Save to disk]
  • Biological Unit Coordinates (2vo5.pdb1.gz) 148 Kb
  • Biological Unit Coordinates (2vo5.pdb2.gz) 149 Kb
  • LPC: Ligand-Protein Contacts for 2VO5
  • CSU: Contacts of Structural Units for 2VO5
  • Likely Quarternary Molecular Structure file(s) for 2VO5
  • Structure Factors (681 Kb)
  • Retrieve 2VO5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VO5 from S2C, [Save to disk]
  • Re-refined 2vo5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VO5 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 2VO5
  • 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 2VO5, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vo5_A] [2vo5] [2vo5_B]
  • SWISS-PROT database: [Q8AAK6]
  • Domain organization of [Q8AAK6_BACTN] by SWISSPFAM
  • Other resources with information on 2VO5
  • Community annotation for 2VO5 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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