4DF3 Crystal Structure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7A date
authors Silva, U.de.
compound source
symmetry
R_factor
R_Free 0.2335
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.73
ligand SAM enzyme
Gene APE
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructure of Aeropyrum pernix fibrillarin in complex with natively bound S-adenosyl-L-methionine at 1.7 A resolution., de Silva U, Zhou Z, Brown BA 2nd, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Aug;68(Pt 8):854-9. Epub, 2012 Jul 26. PMID:22869109
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (4df3.pdb1.gz) 42 Kb
  • Biological Unit Coordinates (4df3.pdb2.gz) 41 Kb
  • LPC: Ligand-Protein Contacts for 4DF3
  • CSU: Contacts of Structural Units for 4DF3
  • Structure Factors (641 Kb)
  • Retrieve 4DF3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4DF3 from S2C, [Save to disk]
  • Re-refined 4df3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4DF3 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 4DF3
  • 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 4DF3, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4df3_B] [4df3] [4df3_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 4DF3: [Fibrillarin ] by SMART
  • Other resources with information on 4DF3
  • Community annotation for 4DF3 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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