4B6S Lyase date Aug 14, 2012
title Structure Of Helicobacter Pylori Type II Dehydroquinase Inhi (2s)-2-Perfluorobenzyl-3-Dehydroquinic Acid
authors J.M.Otero, A.L.Llamas-Saiz, E.Lence, L.Tizon, A.Peon, V.F.V.Praze H.Lamb, A.R.Hawkins, C.Gonzalez-Bello, M.J.Van Raaij
compound source
Molecule: 3-Dehydroquinate Dehydratase
Chain: A, B, C
Synonym: 3-Dehydroquinase, Type II Dhqase
Ec: 4.2.1.10
Engineered: Yes
Organism_scientific: Helicobacter Pylori 26695
Organism_taxid: 85962
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet21a
symmetry Space Group: P 42 2 2
R_factor 0.226 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.190 100.190 104.580 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand 2HN, PO4 enzyme Lyase E.C.4.2.1.10 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceMechanistic Basis of the Inhibition of Type II Dehydroquinase by (2S)- and (2R)-2-Benzyl-3-dehydroquinic Acids., Lence E, Tizon L, Otero JM, Peon A, Prazeres VF, Llamas-Saiz AL, Fox GC, van Raaij MJ, Lamb H, Hawkins AR, Gonzalez-Bello C, ACS Chem Biol. 2012 Dec 6. PMID:23198883
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (4b6s.pdb1.gz) 319 Kb
  • LPC: Ligand-Protein Contacts for 4B6S
  • CSU: Contacts of Structural Units for 4B6S
  • Structure Factors (1825 Kb)
  • Retrieve 4B6S in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4B6S from S2C, [Save to disk]
  • Re-refined 4b6s structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4B6S 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 4B6S
  • 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 4B6S, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4b6s] [4b6s_C] [4b6s_B] [4b6s_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4B6S
  • Community annotation for 4B6S at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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