6GFI

Structure of Human Mesotrypsin in complex with APPI variant T11V/M17R/I18F/F34V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mapping protein selectivity landscapes using multi-target selective screening and next-generation sequencing of combinatorial libraries.

Naftaly, S.Cohen, I.Shahar, A.Hockla, A.Radisky, E.S.Papo, N.

(2018) Nat Commun 9: 3935-3935

  • DOI: 10.1038/s41467-018-06403-x

  • PubMed Abstract: 
  • Characterizing the binding selectivity landscape of interacting proteins is crucial both for elucidating the underlying mechanisms of their interaction and for developing selective inhibitors. However, current mapping methods are laborious and cannot ...

    Characterizing the binding selectivity landscape of interacting proteins is crucial both for elucidating the underlying mechanisms of their interaction and for developing selective inhibitors. However, current mapping methods are laborious and cannot provide a sufficiently comprehensive description of the landscape. Here, we introduce a novel and efficient strategy for comprehensively mapping the binding landscape of proteins using a combination of experimental multi-target selective library screening and in silico next-generation sequencing analysis. We map the binding landscape of a non-selective trypsin inhibitor, the amyloid protein precursor inhibitor (APPI), to each of the four human serine proteases (kallikrein-6, mesotrypsin, and anionic and cationic trypsins). We then use this map to dissect and improve the affinity and selectivity of APPI variants toward each of the four proteases. Our strategy can be used as a platform for the development of a new generation of target-selective probes and therapeutic agents based on selective protein-protein interactions.


    Organizational Affiliation

    Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRSS3 protein
A, B
224Homo sapiensMutation(s): 0 
Gene Names: PRSS3 (PRSS4, TRY3, TRY4)
EC: 3.4.21.4
Find proteins for P35030 (Homo sapiens)
Go to Gene View: PRSS3
Go to UniProtKB:  P35030
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Amyloid-beta A4 protein
E, C
81Homo sapiensMutation(s): 1 
Gene Names: APP (A4, AD1)
Find proteins for P05067 (Homo sapiens)
Go to Gene View: APP
Go to UniProtKB:  P05067
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.301 
  • R-Value Work: 0.245 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 53.215α = 90.00
b = 53.215β = 90.00
c = 237.163γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel2015134

Revision History 

  • Version 1.0: 2018-09-12
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references