3VHH Biotin-Binding Protein date Aug 25, 2011
title Crystal Structure Of Dime-Biotin-Avidin Complex
authors T.Terai, E.Maki, S.Sugiyama, Y.Takahashi, H.Matsumura, Y.Mori, T.N
compound source
Molecule: Avidin
Chain: A, B, C, D
Fragment: Unp Residues 25-147
 Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
symmetry Space Group: C 1 2 1
R_factor 0.200 R_Free 0.260
crystal
cell
length a length b length c angle alpha angle beta angle gamma
129.967 73.510 81.473 90.00 119.64 90.00
method X-Ray Diffractionresolution 2.26 Å
ligand NAG, SO4, VHH enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceRational development of caged-biotin protein-labeling agents and some applications in live cells., Terai T, Maki E, Sugiyama S, Takahashi Y, Matsumura H, Mori Y, Nagano T, Chem Biol. 2011 Oct 28;18(10):1261-72. PMID:22035795
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (87 Kb) [Save to disk]
  • Biological Unit Coordinates (3vhh.pdb1.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 3VHH
  • CSU: Contacts of Structural Units for 3VHH
  • Structure Factors (719 Kb)
  • Retrieve 3VHH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VHH from S2C, [Save to disk]
  • Re-refined 3vhh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3VHH 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 3VHH
  • 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 3VHH, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vhh_B] [3vhh_C] [3vhh_A] [3vhh_D] [3vhh]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3VHH
  • Community annotation for 3VHH at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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