3UPC 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: Heavy Chain Variable Domain
Chain: A, B, C, D, E, F, G, H, I, J
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 21 21 2
R_factor 0.209 R_Free 0.247
length a length b length c angle alpha angle beta angle gamma
82.610 143.120 145.610 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand 1PE, PEG, PG4, PGE enzyme
F, A, J, E, B, H, C, D, I, G

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] (336 Kb) [Save to disk]
  • Biological Unit Coordinates (3upc.pdb1.gz) 36 Kb
  • Biological Unit Coordinates (3upc.pdb2.gz) 36 Kb
  • Biological Unit Coordinates (3upc.pdb3.gz) 36 Kb
  • Biological Unit Coordinates (3upc.pdb4.gz) 36 Kb
  • Biological Unit Coordinates (3upc.pdb5.gz) 34 Kb
  • Biological Unit Coordinates (3upc.pdb6.gz) 35 Kb
  • Biological Unit Coordinates (3upc.pdb7.gz) 36 Kb
  • Biological Unit Coordinates (3upc.pdb8.gz) 36 Kb
  • Biological Unit Coordinates (3upc.pdb9.gz) 35 Kb
  • LPC: Ligand-Protein Contacts for 3UPC
  • CSU: Contacts of Structural Units for 3UPC
  • Structure Factors (2245 Kb)
  • Retrieve 3UPC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UPC from S2C, [Save to disk]
  • Re-refined 3upc structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UPC 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 3UPC
  • 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 3UPC, from MSDmotif at EBI
  • Fold representative 3upc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3upc_D] [3upc_E] [3upc_A] [3upc_G] [3upc_F] [3upc_J] [3upc_I] [3upc_H] [3upc_B] [3upc_C] [3upc]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3UPC: [IGv ] by SMART
  • Other resources with information on 3UPC
  • Community annotation for 3UPC at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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