1ZA3

The crystal structure of the YSd1 Fab bound to DR5

• PDB DOI: https://doi.org/10.2210/pdb1ZA3/pdb

• Classification: IMMUNE SYSTEM/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2005-04-05 Released: 2005-06-14 
• Deposition Author(s): Fellouse, F.A., Li, B., Compaan, D.M., Peden, A.A., Hymowitz, S.G., Sidhu, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.280 
• R-Value Work: 0.224 
• R-Value Observed: 0.230 

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

• PubMed: 15854651 
• DOI: https://doi.org/10.1016/j.jmb.2005.03.041
• Primary Citation of Related Structures:  
  1ZA3


• 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(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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 126.74 kDa 
• Atom Count: 8,149 
• Modelled Residue Count: 1,071 
• Deposited Residue Count: 1,166 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-YSd1 light chain	A, D [auth L]	213	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab-YSd1 heavy chain	B, E [auth H]	236	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 10B	C [auth R], F [auth S]	134	Homo sapiens	Mutation(s): 0  Gene Names: DR5
UniProt & NIH Common Fund Data Resources
Find proteins for O14763 (Homo sapiens) Explore O14763  Go to UniProtKB:  O14763
PHAROS:  O14763 GTEx:  ENSG00000120889

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 0.280 
• R-Value Work: 0.224 
• R-Value Observed: 0.230 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.059	α = 90
b = 147.059	β = 90
c = 144.947	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-14 
Deposition Author(s): Fellouse, F.A., Li, B., Compaan, D.M., Peden, A.A., Hymowitz, S.G., Sidhu, S.S.

Revision History  

• Version 1.0: 2005-06-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2014-02-05
  Changes: Source and taxonomy
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description