SNA1: Ligand sequences with Kd below 10 microM SNA1: Ligand sequences with Kd below 10 microM ERBIN: Ligand sequences with Kd below 10 microM ERBIN: Ligand sequences with Kd below 10 microM AF6: Ligand sequences with Kd below 10 microM AF6: Ligand sequences with Kd below 10 microM AF6/ERBIN/SNA1: Ligand sequences with Kd below 50 microM ERBIN/SNA1: Ligand sequences with Kd below 50 microM AF6/SNA1: Ligand sequences with Kd below 50 microM AF6/ERBIN: Ligand sequences with Kd below 50 microM SNA1: Ligand sequences with Kd below 50 microM SNA1: Ligand sequences with Kd below 50 microM SNA1: Ligand sequences with Kd below 50 microM ERBIN: Ligand sequences with Kd below 50 microM ERBIN: Ligand sequences with Kd below 50 microM AF6: Ligand sequences with Kd below 50 microM AF6: Ligand sequences with Kd below 50 microM AF6: Ligand sequences with Kd below 50 microM AF6: Ligand sequences with Kd below 50 microM AF6/ERBIN/SNA1: Ligand sequences with Kd below 100 microM ERBIN/SNA1: Ligand sequences with Kd below 100 microM AF6/SNA1: Ligand sequences with Kd below 100 microM AF6/ERBIN: Ligand sequences with Kd below 100 microM SNA1: Ligand sequences with Kd below 100 microM SNA1: Ligand sequences with Kd below 100 microM SNA1: Ligand sequences with Kd below 100 microM ERBIN: Ligand sequences with Kd below 100 microM ERBIN: Ligand sequences with Kd below 100 microM AF6: Ligand sequences with Kd below 100 microM AF6: Ligand sequences with Kd below 100 microM AF6: Ligand sequences with Kd below 100 microM AF6: Ligand sequences with Kd below 100 microM



PDZ Domain ligand specificity, affinity and selectivity

The detailed knowledge of the specificity of protein-protein-interaction domains is a prerequisite for understanding the interaction network that is established via these adaptor proteins. The specificity of a protein interaction domain can be expressed in terms of the affinity towards all recognized ligands.
On this site we provide tools to analyze the specificity of three PDZ domains. PDZ domains are protein-protein interaction domains recognizing mainly the C-termini (carboxy-termini) of their target proteins. PDZ domains are named after


Specificity and Affinity Predictions
Ligand affinity predictions are available for the following PDZ domains:
AF6 PDZ domain



AF6 PDZ domain

ALL-1 fusion partner 6
[SwissProt: AF6_HUMAN]

ERBIN PDZ domain



ERBIN PDZ domain

ERB2 interacting protein
[SwissProt: Q9NR18]

SNA1 PDZ domain



SNA1 PDZ domain

alpha-1-Syntrophin
[SwissProt: SNA1_HUMAN]


PDZ domain Selectivity
The selectivity of a domain describes its property of how sharp the recognized ligands are differentiated from the non-recognized or the ones recognized by other domains. This means that the selectivity with respect to the complete potential sequence space is a function of the size of the recognized ligand sequence space. If two or more domains are considered, the selectivity between these domains is a function of the overlap of the recognized ligand sequence spaces.

Below, the recognized ligand sequence spaces are contoured at 10, 50 and 100 micro-molar Kd-tresholds
You can click on the individual areas, respresenting the corresponding sequence spaces, to obtain the list of the underlying affinity sorted ligand sequence.s


Ligand sequence spaces
Kd < 10 micro-molar

PDZ domain selectivity below 10 microM
You can click on the individual areas, respresenting the corresponding sequence spaces, to obtain the list of the underlying affinity sorted ligand sequences. The super-binders are indicated by an asterisk (AF6), a rhombus (ERBIN) and a circle (SNA1).


Ligand sequence spaces
Kd < 50 micro-molar

PDZ domain selectivity below 10 microM
You can click on the individual areas, respresenting the corresponding sequence spaces, to obtain the list of the underlying affinity sorted ligand sequences. The super-binders are indicated by an asterisk (AF6), a rhombus (ERBIN) and a circle (SNA1).
Loading of the larger sequence spaces may take some time due to the large number of sequences!


Ligand sequence spaces
Kd < 100 micro-molar

PDZ domain selectivity below 10 microM
You can click on the individual areas, respresenting the corresponding sequence spaces, to obtain the list of the underlying affinity sorted ligand sequences. The super-binders are indicated by an asterisk (AF6), a rhombus (ERBIN) and a circle (SNA1).
Loading of the larger sequence spaces may take some time due to the large number of sequences!

Reference:
Urs Wiedemann and Prisca Boisguerin, Rainer Leben, Dietmar Leitner, Gerd Krause, Karin Moelling, Rudolf Volkmer-Engert and Hartmut Oschkinat (2004) submitted.

Last modified: Tue May 18 22:54:53 W. Europe Daylight Time 2004

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