9QNE | pdb_00009qne

Streptavidin with a thiophenol cofactor as artificial hydrogen atom transferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

An Asymmetric Hydrogen Atom Transferase with an Abiological Thiophenol Cofactor.

Cao, H.Zhang, K.Gorbachev, V.Vornholt, T.Yu, K.Chen, D.Ward, T.R.

(2025) J Am Chem Soc 147: 41600-41609

  • DOI: https://doi.org/10.1021/jacs.5c12516
  • Primary Citation Related Structures: 
    9QNE, 9QNP, 9QNZ

  • PubMed Abstract: 

    Biocatalytic hydrogen atom transfer (HAT) holds the potential to help address some long-standing challenges in organic synthesis. Although several families of enzymes rely on cysteine to perform HAT, these enzymes are rather impractical for synthetic purposes. To circumvent possible side reactions associated with cysteinyl radicals, we report herein artificial hydrogen atom transferases (AHATases) with an abiological thiophenol cofactor, capitalizing on biotin-streptavidin technology. Chemogenetic optimization afforded an AHATase with good reactivity and high enantioselectivity (er up to 93:7) for the photoinduced radical hydroamination of alkenes. Crystal structures suggest that aromatic-sulfur interactions are key contributing factors to cofactor anchoring and enantioinduction. Mechanistic studies support H atom abstraction and donation processes, both of which are catalyzed by the AHATase. Our work highlights the synthetic potential of thiol-based biocatalytic HAT and expands the repertoire of HAT biocatalysis.


  • Organizational Affiliation
    • Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, Basel 4058, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 17.29 kDa 
  • Atom Count: 1,125 
  • Modeled Residue Count: 125 
  • Deposited Residue Count: 159 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Streptavidin159Streptomyces avidiniiMutation(s): 0 
UniProt
Find proteins for P22629 (Streptomyces avidinii)
Explore P22629 
Go to UniProtKB:  P22629
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22629
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I7Y
(Subject of Investigation/LOI)

Query on A1I7Y



Download:Ideal Coordinates CCD File
B [auth A]5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(3-sulfanylphenyl)pentanamide
C16 H21 N3 O2 S2
HLZRUWZNECQSHZ-YDHLFZDLSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.202 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.388α = 90
b = 57.388β = 90
c = 182.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland200020_212088

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Database references