1D6Z Oxidoreductase date Oct 16, 1999
title Crystal Structure Of The Aerobically Freeze Trapped Rate-Det Catalytic Intermediate Of E. Coli Copper-Containing Amine O
authors C.M.Wilmot, J.Hajdu, M.J.Mcpherson, P.F.Knowles, S.E.V.Phillips
compound source
Molecule: Copper Amine Oxidase
Chain: A, B
Ec: 1.4.3.6
Engineered: Yes
 Organism_scientific: Escherichia Coli
Organism_taxid: 562
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
135.236 166.482 79.628 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CA, CU, GOL, HY1, PEA, PEO, TYY enzyme Oxidoreductase E.C.1.4.3.6 BRENDA
related structures by homologous chain: 1DYU, 1JRQ
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceVisualization of dioxygen bound to copper during enzyme catalysis., Wilmot CM, Hajdu J, McPherson MJ, Knowles PF, Phillips SE, Science 1999 Nov 26;286(5445):1724-8. PMID:10576737
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (261 Kb) [Save to disk]
  • Biological Unit Coordinates (1d6z.pdb1.gz) 255 Kb
  • LPC: Ligand-Protein Contacts for 1D6Z
  • CSU: Contacts of Structural Units for 1D6Z
  • Likely Quarternary Molecular Structure file(s) for 1D6Z
  • Structure Factors (732 Kb)
  • Retrieve 1D6Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D6Z from S2C, [Save to disk]
  • Re-refined 1d6z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1D6Z 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 1D6Z
  • 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 1D6Z, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d6za3, region A:186-300 [Jmol] [rasmolscript] [script source]
        - Domain d1d6za1, region A:301-724 [Jmol] [rasmolscript] [script source]
        - Domain d1d6za4, region A:7-90 [Jmol] [rasmolscript] [script source]
        - Domain d1d6za2, region A:91-185 [Jmol] [rasmolscript] [script source]
        - Domain d1d6zb3, region B:186-300 [Jmol] [rasmolscript] [script source]
        - Domain d1d6zb1, region B:301-725 [Jmol] [rasmolscript] [script source]
        - Domain d1d6zb4, region B:6-90 [Jmol] [rasmolscript] [script source]
        - Domain d1d6zb2, region B:91-185 [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: [1d6z_A] [1d6z_B] [1d6z]
  • SWISS-PROT database: [P46883]
  • Domain organization of [AMO_ECOLI] by SWISSPFAM
    • Other resources with information on 1D6Z
  • Community annotation for 1D6Z 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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