1DB3 Lyase date Nov 02, 1999
title E.Coli Gdp-Mannose 4,6-Dehydratase
authors J.R.Somoza, S.Menon, W.S.Somers, F.X.Sullivan
compound source
Molecule: Gdp-Mannose 4,6-Dehydratase
Chain: A
Ec: 4.2.1.47
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pt7gmd
symmetry Space Group: P 63 2 2
R_factor 0.205 R_Free 0.232
crystal
cell
length a length b length c angle alpha angle beta angle gamma
149.600 149.600 102.600 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand
enzyme Lyase E.C.4.2.1.47 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose., Somoza JR, Menon S, Schmidt H, Joseph-McCarthy D, Dessen A, Stahl ML, Somers WS, Sullivan FX, Structure Fold Des 2000 Feb 15;8(2):123-35. PMID:10673432
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (1db3.pdb1.gz) 109 Kb
  • CSU: Contacts of Structural Units for 1DB3
  • Likely Quarternary Molecular Structure file(s) for 1DB3
  • Structure Factors (255 Kb)
  • Retrieve 1DB3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DB3 from S2C, [Save to disk]
  • Re-refined 1db3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DB3 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 1DB3
  • 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 1DB3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1db3a_, 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: [1db3] [1db3_A]
  • SWISS-PROT database: [P0AC88]
  • Domain organization of [GM4D_ECOLI] by SWISSPFAM
  • Other resources with information on 1DB3
  • Community annotation for 1DB3 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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