Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 4-mer -A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48024.03 
• Atom Count: 3378 
• Residue Count: 440 
• Unique protein chains: 2

1VPO

Crystal Structure Analysis of the Anti-testosterone Fab in Complex with Testosterone

• DOI: 10.2210/pdb1VPO/pdb
• Entry 1VPO supersedes 1L7S

• Classification: IMMUNE SYSTEM
• Expression System: Escherichia coli


• Deposited: 2004-11-15 Released: 2004-11-23 
• Deposition Author(s): Valjakka, J.M., Hemminki, A., Niemi, S., Soderlund, H., Takkinen, K., Rouvinen, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.274 
• R-Value Work: 0.211 

Literature

Crystal Structure of an in Vitro Affinity- and Specificity-matured Anti-testosterone Fab in Complex with Testosterone. IMPROVED AFFINITY RESULTS FROM SMALL STRUCTURAL CHANGES WITHIN THE VARIABLE DOMAINS

Valjakka, J.M., Hemminki, A., Niemi, S., Soderlund, H., Takkinen, K., Rouvinen, J.

(2002) J.Biol.Chem. 277: 44021-44027

• PubMed: 12196551 
• DOI: 10.1074/jbc.M208392200
• Primary Citation of Related Structures:  
  1L7T, 1L7S


• PubMed Abstract: 
  

A highly selective, high affinity recombinant anti-testosterone Fab fragment has been generated by stepwise optimization of the complementarity-determining regions (CDRs) by random mutagenesis and phage display selection of a monoclonal antibody (3-C(4)F(5)). The best mutant (77 Fab) was obtained by evaluating the additivity effects of different independently selected CDR mutations. The 77 Fab contains 20 mutations and has about 40-fold increased affinity (K(d) = 3 x 10(-10) m) when compared with the wild-type (3-C(4)F(5)) Fab. To obtain structural insight into factors, which are needed to improve binding properties, we have determined the crystal structures of the mutant 77 Fab fragment with (2.15 A) and without testosterone (2.10 A) and compared these with previously determined wild-type structures. The overall testosterone binding of the 77 Fab is similar to that of the wild-type. The improved affinity and specificity of the 77 Fab fragment are due to more comprehensive packing of the testosterone with the protein, which is the result of small structural changes within the variable domains. Only one important binding site residue Glu-95 of the heavy chain CDR3 is mutated to alanine in the 77 Fab fragment. This mutation, originally selected from the phage library based on improved specificity, provides more free space for the testosterone D-ring. The light chain CDR1 of 77 Fab containing eight mutations has the most significant effect on the improved affinity, although it has no direct contact with the testosterone. The mutations of CDR-L1 cause a rearrangement in its conformation, leading to an overall fine reshaping of the binding site.

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Organizational Affiliation: 

Department of Chemistry, University of Joensuu, P. O. Box 111, Finland. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
anti-testosterone (light chain)	L	219	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
anti-testosterone (heavy chain)	H	221	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
TES	H	TESTOSTERONE C19 H28 O2 MUMGGOZAMZWBJJ-DYKIIFRCSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
TES	Kd: 3000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.274 
• R-Value Work: 0.211 
• Space Group: P 6₂

Unit Cell:

Length (Å)	Angle (°)
a = 82.252	α = 90.00
b = 82.252	β = 90.00
c = 120.059	γ = 120.00

Software Package:

Software Name	Purpose
CNS	phasing
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-11-15 
• Released Date: 2004-11-23 
• Deposition Author(s): Valjakka, J.M., Hemminki, A., Niemi, S., Soderlund, H., Takkinen, K., Rouvinen, J.
• This entry supersedes: 1L7S

Revision History 

• Version 1.0: 2004-11-23
  Type: Initial release
• Version 1.1: 2008-04-26
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2018-04-04
  Type: Data collection