2GVK Crystal structure of a dye-decolorizing peroxidase (DyP) from Bacteroides thetaiotaomicron VPI-5482 at 1.6 A resolution date
authors JCSG, Joint.Center.for.Structural.Genomics.
compound source
symmetry
R_factor
R_Free 0.19
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.60
ligand ACY, CL, EDO, MSE, NA, UNL enzyme
Gene BT
Gene
Ontology
ChainFunctionProcessComponent
A
  • peroxidase activity


    • Primary referenceCrystal structures of two novel dye-decolorizing peroxidases reveal a beta-barrel fold with a conserved heme-binding motif., Zubieta C, Krishna SS, Kapoor M, Kozbial P, McMullan D, Axelrod HL, Miller MD, Abdubek P, Ambing E, Astakhova T, Carlton D, Chiu HJ, Clayton T, Deller MC, Duan L, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Hampton E, Han GW, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Reyes R, Rife CL, Schimmel P, van den Bedem H, Weekes D, White A, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA, Proteins. 2007 Nov 1;69(2):223-33. PMID:17654545
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (2gvk.pdb1.gz) 340 Kb
  • LPC: Ligand-Protein Contacts for 2GVK
  • CSU: Contacts of Structural Units for 2GVK
  • Likely Quarternary Molecular Structure file(s) for 2GVK
  • Structure Factors (19740 Kb)
  • Retrieve 2GVK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2GVK from S2C, [Save to disk]
  • Re-refined 2gvk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2GVK 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 2GVK
  • 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 2GVK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2gvk] [2gvk_A]
  • SWISS-PROT database: [Q8A8E8]
  • Domain organization of [Q8A8E8_BACTN] by SWISSPFAM
    • Other resources with information on 2GVK
  • Community annotation for 2GVK at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science