8TFP | pdb_00008tfp

Fab from C10-S66K antibody in complex with carfentanil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8TFP

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity That Reverses Carfentanil-Induced Respiratory Depression.

Eubanks, L.M.Pholcharee, T.Oyen, D.Natori, Y.Zhou, B.Wilson, I.A.Janda, K.D.

(2023) ACS Chem Neurosci 14: 2849-2856

  • DOI: https://doi.org/10.1021/acschemneuro.3c00455
  • Primary Citation Related Structures: 
    8TFP, 8TFQ, 8TFR

  • PubMed Abstract: 

    The opioid overdose crisis primarily driven by potent synthetic opioids resulted in more than 500,000 deaths in the US over the last 20 years. Though naloxone, a short-acting medication, remains the primary treatment option for temporarily reversing opioid overdose effects, alternative countermeasures are needed. Monoclonal antibodies present a versatile therapeutic opportunity that can be tailored to synthetic opioids and help prevent post-treatment renarcotization. The ultrapotent analog carfentanil is especially concerning due to its unique pharmacological properties. With this in mind, we generated a fully human antibody through a drug-specific B cell sorting strategy with a combination of carfentanil and fentanyl probes. The resulting pan-specific antibody was further optimized through scFv phage display, producing C10-S66K. This monoclonal antibody displays high affinity to carfentanil, fentanyl, and other analogs and reversed carfentanil-induced respiratory depression. Additionally, X-ray crystal structures with carfentanil and fentanyl bound provided structural insight into key drug:antibody interactions.

Macromolecule Content 

  • Total Structure Weight: 94.25 kDa 
  • Atom Count: 7,334 
  • Modeled Residue Count: 853 
  • Deposited Residue Count: 874 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of Fab from C10-S66K antibodyA,
B [auth L]
214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of Fab from C10-S66K antibodyC [auth B],
D [auth H]
223Homo sapiensMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.05α = 90
b = 73.492β = 90.38
c = 95.089γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesU01DA046232

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release
  • Version 1.1: 2023-08-23
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Derived calculations, Structure summary
  • Version 1.3: 2024-11-20
    Changes: Structure summary