3DOY Lyase date Jul 07, 2008
title Crystal Structure Of (3r)-Hydroxyacyl-Acyl Carrier Protein D (Fabz) From Helicobacter Pylori In Complex With Compound 3i
authors L.Zhang, L.He, X.Liu, H.Liu, X.Shen, H.Jiang
compound source
Molecule: (3r)-Hydroxymyristoyl-Acyl Carrier Protein Dehydr
Chain: A, B, C, D, E, F
Ec: 4.2.1.-
Engineered: Yes
Organism_scientific: Helicobacter Pylori
Organism_common: Campylobacter Pylori
Organism_taxid: 210
Strain: Ss1
Gene: Fabz
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: M15
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pqe30
symmetry Space Group: P 21 21 21
R_factor 0.200 R_Free 0.238
crystal
cell
length a length b length c angle alpha angle beta angle gamma
73.975 100.370 186.622 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand 2BE, BEN, CL BindingDB enzyme Lyase E.C.4.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceDiscovering potent inhibitors against the beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) of Helicobacter pylori: structure-based design, synthesis, bioassay, and crystal structure determination., He L, Zhang L, Liu X, Li X, Zheng M, Li H, Yu K, Chen K, Shen X, Jiang H, Liu H, J Med Chem. 2009 Apr 23;52(8):2465-81. PMID:19309082
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • Biological Unit Coordinates (3doy.pdb1.gz) 153 Kb
  • LPC: Ligand-Protein Contacts for 3DOY
  • CSU: Contacts of Structural Units for 3DOY
  • Likely Quarternary Molecular Structure file(s) for 3DOY
  • Structure Factors (2818 Kb)
  • Retrieve 3DOY in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DOY from S2C, [Save to disk]
  • Re-refined 3doy structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DOY 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 3DOY
  • 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 3DOY, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3doy_A] [3doy_E] [3doy] [3doy_C] [3doy_B] [3doy_F] [3doy_D]
  • SWISS-PROT database: [Q5G940]
  • Domain organization of [Q5G940_HELPY] by SWISSPFAM
  • Other resources with information on 3DOY
  • Community annotation for 3DOY 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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