9AXQ | pdb_00009axq

Crystal Structure of HY11-7E1_Hu3 Fab in the Apo Conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure-Based Engineering of Monoclonal Antibodies for Improved Binding to Counteract the Effects of Fentanyl and Carfentanil.

Rodarte, J.Baehr, C.Hicks, D.McGovern, M.Zhang, Y.Silva-Ortiz, P.Hannon, B.Duddu, S.Pancera, M.Pravetoni, M.

(2024) ACS Omega 9: 42506-42519

  • DOI: https://doi.org/10.1021/acsomega.4c06617
  • Primary Citation of Related Structures:  
    9AXN, 9AXO, 9AXP, 9AXQ, 9AXR, 9AXS

  • PubMed Abstract: 

    The opioid overdose epidemic is a growing and evolving public health crisis fueled by the widespread presence of fentanyl and fentanyl analogues (F/FAs) in both street mixtures and counterfeit pills. To expand current treatment options, drug-targeting monoclonal antibodies (mAbs) offer a viable therapeutic for both pre- and postexposure clinical scenarios. This study reports the isolation, in vitro characterization, and in vivo efficacy of two murine mAb families targeting fentanyl, carfentanil, or both. Because humanization of the mAbs by CDR grafting negatively impacted affinity for both fentanyl and carfentanil, crystal structures of mAbs in complex with fentanyl or carfentanil were analyzed to identify key residues involved in ligand binding in murine versus humanized structures, and site-directed mutagenesis was used to verify their functional importance. The structural analysis identified a framework residue, Tyr36, present in the murine germline sequence of two mAbs, which was critical for binding to fentanyl and carfentanil. These studies emphasize the importance of structural considerations in mAb engineering to optimize mAbs targeting small molecules including opioids and other drugs of public health interest.


  • Organizational Affiliation

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HY11-7E1_Hu3 Fab Heavy ChainA [auth H],
C [auth A],
D [auth C],
E
232Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HY11-7E1_Hu3 Fab Light ChainB [auth L],
F [auth B],
G [auth D],
H [auth F]
214Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth L],
K [auth L],
T [auth F],
U [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth H]
L
M [auth L]
N [auth A]
O [auth C]
I [auth H],
L,
M [auth L],
N [auth A],
O [auth C],
P [auth B],
Q [auth B],
R [auth D],
S [auth D],
V [auth F],
W [auth F]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
A [auth H],
C [auth A],
D [auth C],
E
L-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.238 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.581α = 90
b = 151.103β = 91.14
c = 104.604γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesUG3 DA047711

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Structure summary
  • Version 1.2: 2025-03-12
    Changes: Database references