3F12 Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus date
authors Thomson, C.A., Bryson, S., McLean, G.R., Creagh, A.L., Pai, E.F., Schrader, J.W.
compound source
R_Free 0.32
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.95
Primary referenceGermline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus., Thomson CA, Bryson S, McLean GR, Creagh AL, Pai EF, Schrader JW, EMBO J. 2008 Oct 8;27(19):2592-602. Epub 2008 Sep 4. PMID:18772881
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (135 Kb) [Save to disk]
  • Biological Unit Coordinates (3f12.pdb1.gz) 65 Kb
  • Biological Unit Coordinates (3f12.pdb2.gz) 66 Kb
  • CSU: Contacts of Structural Units for 3F12
  • Structure Factors (436 Kb)
  • Retrieve 3F12 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3F12 from S2C, [Save to disk]
  • Re-refined 3f12 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3F12 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 3F12
  • 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 3F12, from MSDmotif at EBI
  • Fold representative 3f12 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3f12_A] [3f12_C] [3f12_B] [3f12_D] [3f12]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3F12: [IG_like] [IGv ] by SMART
  • Other resources with information on 3F12
  • Community annotation for 3F12 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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