1ZA3

The crystal structure of the YSd1 Fab bound to DR5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular recognition by a binary code.

Fellouse, F.A.Li, B.Compaan, D.M.Peden, A.A.Hymowitz, S.G.Sidhu, S.S.

(2005) J.Mol.Biol. 348: 1153-1162

  • DOI: 10.1016/j.jmb.2005.03.041

  • PubMed Abstract: 
  • Functional antibodies were obtained from a library of antigen-binding sites generated by a binary code restricted to tyrosine and serine. An antibody raised against human vascular endothelial growth factor recognized the antigen with high affinity (K ...

    Functional antibodies were obtained from a library of antigen-binding sites generated by a binary code restricted to tyrosine and serine. An antibody raised against human vascular endothelial growth factor recognized the antigen with high affinity (K(D)=60 nM) and high specificity in cell-based assays. The crystal structure of another antigen binding fragment in complex with its antigen (human death receptor DR5) revealed the structural basis for this minimalist mode of molecular recognition. Natural antigen-binding sites are enriched for tyrosine and serine, and we show that these amino acid residues are intrinsically well suited for molecular recognition. Furthermore, these results demonstrate that molecular recognition can evolve from even the simplest chemical diversity.


    Organizational Affiliation

    Department of Protein Engineering, Genentech Inc, 1 DNA Way, South San Francisco, CA 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab-YSd1 light chain
A, L
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab-YSd1 heavy chain
B, H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor receptor superfamily member 10B
R, S
134Homo sapiensMutation(s): 0 
Gene Names: TNFRSF10B (DR5, KILLER, TRAILR2, TRICK2, ZTNFR9)
Find proteins for O14763 (Homo sapiens)
Go to Gene View: TNFRSF10B
Go to UniProtKB:  O14763
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 147.059α = 90.00
b = 147.059β = 90.00
c = 144.947γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2014-02-05
    Type: Source and taxonomy