3V56 Immune System date Dec 16, 2011
title Re-Refinement Of Pdb Entry 1osg - Complex Between Baff And A Derived Peptide Presented In A Beta-Hairpin Scaffold - Reve Additonal Copy Of The Peptide.
authors O.S.Smart, T.O.Womack, C.Flensburg, P.Keller, A.Sharff, W.Paciore C.Vonrhein, G.Bricogne
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, C, D, E, F
Synonym: B Lymphocyte Stimulator, Blys, B-Cell-Activating F Baff, Dendritic Cell-Derived Tnf-Like Molecule, Tnf- And Ap Leukocyte Expressed Ligand 1, Tall-1, Tumor Necrosis Factor Superfamily Member 13b, Membrane Form, Tumor Necrosis Facto Superfamily Member 13b, Soluble Form;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfsf13b, Baff, Blys, Tall1, Tnfsf20, Ztnf4, Unq401p
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b

Molecule: Br3 Derived Peptive
Chain: G, H, I, J, K, L, Z
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 65
R_factor 0.162 R_Free 0.200
length a length b length c angle alpha angle beta angle gamma
121.633 121.633 157.214 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand ACE, NH2, SO4 enzyme
F, A, D, C, E, B

Primary referenceExploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER., Smart OS, Womack TO, Flensburg C, Keller P, Paciorek W, Sharff A, Vonrhein C, Bricogne G, Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):368-80. Epub 2012 Mar 16. PMID:22505257
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (324 Kb) [Save to disk]
  • Biological Unit Coordinates (3v56.pdb1.gz) 156 Kb
  • Biological Unit Coordinates (3v56.pdb2.gz) 157 Kb
  • Biological Unit Coordinates (3v56.pdb3.gz) 7 Kb
  • LPC: Ligand-Protein Contacts for 3V56
  • CSU: Contacts of Structural Units for 3V56
  • Structure Factors (977 Kb)
  • Retrieve 3V56 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3V56 from S2C, [Save to disk]
  • Re-refined 3v56 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3V56 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 3V56
  • 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 3V56, from MSDmotif at EBI
  • Fold representative 3v56 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3v56_E] [3v56_A] [3v56_B] [3v56_Z] [3v56_J] [3v56_K] [3v56_L] [3v56] [3v56_D] [3v56_I] [3v56_G] [3v56_F] [3v56_C] [3v56_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3V56: [TNF ] by SMART
  • Other resources with information on 3V56
  • Community annotation for 3V56 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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