5TZO

Computationally Designed Fentanyl Binder - Fen49*-Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Computational design of environmental sensors for the potent opioid fentanyl.

Bick, M.J., Greisen, P.J., Morey, K.J., Antunes, M.S., La, D., Sankaran, B., Reymond, L., Johnsson, K., Medford, J.I., Baker, D.

(2017) Elife 6

  • DOI: 10.7554/eLife.28909
  • Primary Citation of Related Structures:  
    5TVV, 5TVY, 5TZO

  • PubMed Abstract: 

    • We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity ...

    We describe the computational design of proteins that bind the potent analgesic fentanyl. Our approach employs a fast docking algorithm to find shape complementary ligand placement in protein scaffolds, followed by design of the surrounding residues to optimize binding affinity. Co-crystal structures of the highest affinity binder reveal a highly preorganized binding site, and an overall architecture and ligand placement in close agreement with the design model. We use the designs to generate plant sensors for fentanyl by coupling ligand binding to design stability. The method should be generally useful for detecting toxic hydrophobic compounds in the environment.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, University of Washington, Seattle, United States.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endo-1,4-beta-xylanase AA, B, C188Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: xynA, BSU18840
EC: 3.2.1.8
UniProt
Find proteins for P18429 (Bacillus subtilis (strain 168))
Explore P18429 
Go to UniProtKB:  P18429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18429
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
7V7 Binding MOAD:  5TZO Kd: 5900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.07α = 90
b = 73.25β = 90
c = 136.64γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5F32CA171572-03
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1-13-1-0054
Life Sciences Discovery FundUnited States9598385

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence