3OVJ Protein Fibril date Sep 16, 2010
title Structure Of An Amyloid Forming Peptide Klvffa From Amyloid Complex With Orange G
authors M.Landau, D.Eisenberg
compound source
Molecule: Klvffa Hexapeptide Segment From Amyloid Beta
Chain: A, B, C, D
Fragment: Klvffa (Unp Residues 687-692)
Engineered: Yes
 Synthetic: Yes
Organism_taxid: 32630
Other_details: Klvffa (Residues 16-21) From Amyloid Beta, Synthesized
symmetry Space Group: P 1
R_factor 0.205 R_Free 0.220
crystal
cell
length a length b length c angle alpha angle beta angle gamma
9.536 26.008 25.803 62.28 88.59 88.45
method X-Ray Diffractionresolution 1.80 Å
ligand ORA enzyme
Primary referenceTowards a pharmacophore for amyloid., Landau M, Sawaya MR, Faull KF, Laganowsky A, Jiang L, Sievers SA, Liu J, Barrio JR, Eisenberg D, PLoS Biol. 2011 Jun;9(6):e1001080. Epub 2011 Jun 14. PMID:21695112
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (10 Kb) [Save to disk]
  • Biological Unit Coordinates (3ovj.pdb1.gz) 6 Kb
  • LPC: Ligand-Protein Contacts for 3OVJ
  • CSU: Contacts of Structural Units for 3OVJ
  • Structure Factors (27 Kb)
  • Retrieve 3OVJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3OVJ from S2C, [Save to disk]
  • Re-refined 3ovj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3OVJ 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 3OVJ
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3OVJ, from MSDmotif at EBI
  • Fold representative 3ovj from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ovj_A] [3ovj_B] [3ovj_C] [3ovj_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3OVJ with the sequences similar proteins can be viewed for 3OVJ's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
    • Other resources with information on 3OVJ
  • Community annotation for 3OVJ at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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