5AWV Oxidoreductase Antibiotic date Jul 09, 2015
title Crystal Structure Of Glycopeptide Hexose Oxidase Dbv29 Compl Teicoplanin
authors Y.C.Liu, T.L.Li
compound source
Molecule: Putative Hexose Oxidase
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Nonomuraea Sp. Atcc 39727
Organism_taxid: 93944
Gene: Dbv29
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Teicoplanin
Chain: I, J, K, L, M, N, O, P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Actinoplanes Teichomyceticus
Organism_taxid: 1867
symmetry Space Group: P 1 21 1
R_factor 0.156 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.791 150.778 124.853 90.00 98.40 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand 3FG, 3MY, CIT, FAD, GHP, MAN, N1L, NAG, OMY, T55 enzyme
note 5AWV supersedes 4K3T, 2WDX
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceInterception of teicoplanin oxidation intermediates yields new antimicrobial scaffolds., Liu YC, Li YS, Lyu SY, Hsu LJ, Chen YH, Huang YT, Chan HC, Huang CJ, Chen GH, Chou CC, Tsai MD, Li TL, Nat Chem Biol. 2011 May;7(5):304-9. Epub 2011 Apr 10. PMID:21478878
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (374 Kb) [Save to disk]
  • Biological Unit Coordinates (5awv.pdb1.gz) 358 Kb
  • LPC: Ligand-Protein Contacts for 5AWV
  • CSU: Contacts of Structural Units for 5AWV
  • Structure Factors (3050 Kb)
  • Retrieve 5AWV in mmCIF format [Save to disk]
  • Re-refined 5awv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5AWV 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 5AWV
  • 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
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5awv] [5awv_L] [5awv_N] [5awv_K] [5awv_A] [5awv_O] [5awv_D] [5awv_I] [5awv_B] [5awv_J] [5awv_P] [5awv_M] [5awv_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5AWV
  • Community annotation for 5AWV at PDBWiki (http://pdbwiki.org)

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