1DJ9 Transferase date Dec 02, 1999
title Crystal Structure Of 8-Amino-7-Oxonanoate Synthase (Or 7-Ket 8aminipelargonate Or Kapa Synthase) Complexed With Plp And Product 8(S)-Amino-7-Oxonanonoate (Or Kapa). The Enzyme Of Biosynthetic Pathway.
authors S.P.Webster, D.Alexeev, D.J.Campopiano, R.M.Watt, M.Alexeeva, L.S R.L.Baxter
compound source
Molecule: 8-Amino-7-Oxononanoate Synthase
Chain: A
Synonym: 7-Kap Synthetase
Ec: 2.3.1.47
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
symmetry Space Group: P 31 1 2
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.890 58.890 201.770 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.00 Å
ligand KAM, MG, SO4 enzyme Transferase E.C.2.3.1.47 BRENDA
related structures by homologous chain: 1DJE
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceMechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies., Webster SP, Alexeev D, Campopiano DJ, Watt RM, Alexeeva M, Sawyer L, Baxter RL, Biochemistry 2000 Jan 25;39(3):516-28. PMID:10642176
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (72 Kb) [Save to disk]
  • Biological Unit Coordinates (1dj9.pdb1.gz) 67 Kb
  • Biological Unit Coordinates (1dj9.pdb2.gz) 131 Kb
  • LPC: Ligand-Protein Contacts for 1DJ9
  • CSU: Contacts of Structural Units for 1DJ9
  • Likely Quarternary Molecular Structure file(s) for 1DJ9
  • Retrieve 1DJ9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DJ9 from S2C, [Save to disk]
    • View 1DJ9 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 1DJ9
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1DJ9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dj9a_, 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: [1dj9] [1dj9_A]
  • SWISS-PROT database: [P12998]
  • Domain organization of [BIOF_ECOLI] by SWISSPFAM
    • Other resources with information on 1DJ9
  • Community annotation for 1DJ9 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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