3UPA Immune System date Nov 17, 2011
title A General Strategy For The Generation Of Human Antibody Vari Domains With Increased Aggregation Resistance
authors K.Dudgeon, R.Rouet, I.Kokmeijer, D.B.Langley, D.Christ
compound source
Molecule: Kappa Light Chain Variable Domain
Chain: A, B
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Tg1
Expression_system_vector_type: Phagemid
Expression_system_plasmid: Phen1
symmetry Space Group: P 43 21 2
R_factor 0.229 R_Free 0.283
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.040 45.040 173.240 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceGeneral strategy for the generation of human antibody variable domains with increased aggregation resistance., Dudgeon K, Rouet R, Kokmeijer I, Schofield P, Stolp J, Langley D, Stock D, Christ D, Proc Natl Acad Sci U S A. 2012 Jul 3;109(27):10879-84. Epub 2012 Jun 27. PMID:22745168
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (67 Kb) [Save to disk]
  • Biological Unit Coordinates (3upa.pdb1.gz) 32 Kb
  • Biological Unit Coordinates (3upa.pdb2.gz) 32 Kb
  • CSU: Contacts of Structural Units for 3UPA
  • Structure Factors (911 Kb)
  • Retrieve 3UPA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UPA from S2C, [Save to disk]
  • Re-refined 3upa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3UPA 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 3UPA
  • 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 3UPA, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3upa] [3upa_A] [3upa_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3UPA: [IGv ] by SMART
    • Other resources with information on 3UPA
  • Community annotation for 3UPA at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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