5TZO | pdb_00005tzo

Computationally Designed Fentanyl Binder - Fen49*-Complex

• PDB DOI: https://doi.org/10.2210/pdb5TZO/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-22 Released: 2017-10-04 
• Deposition Author(s): 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.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), Defense Threat Reduction Agency (DTRA), Life Sciences Discovery Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.203 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

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

• PubMed: 28925919 
• DOI: https://doi.org/10.7554/eLife.28909
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, United States.
Department of Biology, Colorado State University, Fort Collins, United States.
Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, United States.
Ecole Polytechnique Fédérale de Lausanne, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland.
Department of Chemical Biology, Max-Planck-Institute for Medical Research, Heidelberg, Germany.
Howard Hughes Medical Institute, University of Washington, Seattle, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.54 kDa 
• Atom Count: 5,280 
• Modeled Residue Count: 555 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase A	A, B, C	188	Bacillus subtilis subsp. subtilis str. 168	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7V7	D [auth A], E [auth A], I [auth B], J [auth B], M [auth C], N [auth C]	N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide C22 H28 N2 O PJMPHNIQZUBGLI-UHFFFAOYSA-N
K	F [auth A], G [auth A], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	H [auth A], K [auth B], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.203 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.07	α = 90
b = 73.25	β = 90
c = 136.64	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-10-04 
Deposition Author(s): 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.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5F32CA171572-03
Defense Threat Reduction Agency (DTRA)	United States	HDTRA1-13-1-0054
Life Sciences Discovery Fund	United States	9598385

Revision History  

• 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
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations