2PD7 Circadian Clock Protein date Mar 31, 2007
title 2.0 Angstrom Crystal Structure Of The Fungal Blue-Light Phot Vivid
authors B.D.Zoltowski, B.R.Crane, A.M.Bilwes
compound source
Molecule: Vivid Pas Protein Vvd
Chain: A, B
Fragment: Residues 37-184
Synonym: Hypothetical Protein Ncu03967.1
Engineered: Yes
 Organism_scientific: Neurospora Crassa
Organism_taxid: 5141
Gene: Vvd, G17a4.050
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21de3
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 1 21 1
R_factor 0.245 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.350 80.700 58.570 90.00 95.76 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand FAD enzyme
note 2PD7 (Molecule of the Month:pdb183)
Primary referenceConformational switching in the fungal light sensor Vivid., Zoltowski BD, Schwerdtfeger C, Widom J, Loros JJ, Bilwes AM, Dunlap JC, Crane BR, Science. 2007 May 18;316(5827):1054-7. PMID:17510367
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (2pd7.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (2pd7.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 2PD7
  • CSU: Contacts of Structural Units for 2PD7
  • Likely Quarternary Molecular Structure file(s) for 2PD7
  • Structure Factors (164 Kb)
  • Retrieve 2PD7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2PD7 from S2C, [Save to disk]
  • Re-refined 2pd7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2PD7 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 2PD7
  • 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 2PD7, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2pd7] [2pd7_A] [2pd7_B]
  • SWISS-PROT database: [Q9C3Y6]
  • Domain organization of [Q9C3Y6_NEUCR] by SWISSPFAM
  • Domain found in 2PD7: [PAC ] by SMART
    • Other resources with information on 2PD7
  • Community annotation for 2PD7 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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