5DFW Cell Adhesion date Aug 27, 2015
title Crystal Structure Of Human Cd81 Large Extracellular Loop In With Single Chain Fv Fragment K13
authors S.F.Harris, A.Villasenor, A.Kuglstatter
compound source
Molecule: Cd81 Antigen
Chain: A
Fragment: Unp Residues 112-201
Synonym: 26 Kda Cell Surface Protein Tapa-1,Target Of The Antiproliferative Antibody 1,Tetraspanin-28,Tspan-28;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd81, Tapa1, Tspan28
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Single Chain Fv Fragment
Chain: H
Fragment: Unp Residues 101-810
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 2 1
R_factor 0.190 R_Free 0.264
length a length b length c angle alpha angle beta angle gamma
49.652 49.671 80.452 90.00 105.30 90.00
method X-Ray Diffractionresolution 2.33 Å

Primary referenceVH-VL orientation prediction for antibody humanization candidate selection: A case study., Bujotzek A, Lipsmeier F, Harris SF, Benz J, Kuglstatter A, Georges G, MAbs. 2015 Dec 4:0. PMID:26637054
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (55 Kb) [Save to disk]
  • Biological Unit Coordinates (5dfw.pdb1.gz) 101 Kb
  • CSU: Contacts of Structural Units for 5DFW
  • Structure Factors (371 Kb)
  • Retrieve 5DFW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5DFW from S2C, [Save to disk]
  • Re-refined 5dfw structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5DFW 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 5DFW
  • 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
  • Fold representative 5dfw from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5dfw] [5dfw_A] [5dfw_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5DFW: [IGv ] by SMART
  • Other resources with information on 5DFW
  • Community annotation for 5DFW at PDBWiki (http://pdbwiki.org)

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