1XXM

The modular architecture of protein-protein binding site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The modular architecture of protein-protein binding interfaces

Reichmann, D.Rahat, O.Albeck, S.Meged, R.Dym, O.Schreiber, G.

(2005) Proc.Natl.Acad.Sci.USA 102: 57-62

  • DOI: 10.1073/pnas.0407280102
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein-protein interactions are essential for life. Yet, our understanding of the general principles governing binding is not complete. In the present study, we show that the interface between proteins is built in a modular fashion; each module is c ...

    Protein-protein interactions are essential for life. Yet, our understanding of the general principles governing binding is not complete. In the present study, we show that the interface between proteins is built in a modular fashion; each module is comprised of a number of closely interacting residues, with few interactions between the modules. The boundaries between modules are defined by clustering the contact map of the interface. We show that mutations in one module do not affect residues located in a neighboring module. As a result, the structural and energetic consequences of the deletion of entire modules are surprisingly small. To the contrary, within their module, mutations cause complex energetic and structural consequences. Experimentally, this phenomenon is shown on the interaction between TEM1-beta-lactamase and beta-lactamase inhibitor protein (BLIP) by using multiple-mutant analysis and x-ray crystallography. Replacing an entire module of five interface residues with Ala created a large cavity in the interface, with no effect on the detailed structure of the remaining interface. The modular architecture of binding sites, which resembles human engineering design, greatly simplifies the design of new protein interactions and provides a feasible view of how these interactions evolved.


    Organizational Affiliation

    Departments of Biological Chemistry and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase TEM
A, B
263Escherichia coliMutation(s): 3 
Gene Names: bla, blaT-3, blaT-4, blaT-5, blaT-6
EC: 3.5.2.6
Find proteins for P62593 (Escherichia coli)
Go to UniProtKB:  P62593
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Beta-lactamase inhibitory protein
C, D
165Streptomyces clavuligerusMutation(s): 3 
Find proteins for P35804 (Streptomyces clavuligerus)
Go to UniProtKB:  P35804
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.706α = 90.00
b = 124.473β = 90.00
c = 156.951γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance