9AXR

Crystal Structure of HY18-5B1_Ch Fab in Complex with Fentanyl

• PDB DOI: https://doi.org/10.2210/pdb9AXR/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-03-06 Released: 2024-10-02 
• Deposition Author(s): McGovern, M.R., Rodarte, J.V., Pancera, M.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.316 
• R-Value Work: 0.278 
• R-Value Observed: 0.297 

Starting Model: experimental

Literature

Structure-based engineering of monoclonal antibodies against fentanyl and carfentanil for improved binding

Rodarte, J.V., Pravetoni, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 145.9 kDa 
• Atom Count: 9,156 
• Modelled Residue Count: 1,299 
• Deposited Residue Count: 1,335 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HY18-5B1_Ch Fab Heavy Chain	A, C [auth H], E [auth C]	231	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HY18-5B1_Ch Fab Light Chain	B, D [auth L], F [auth D]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7V7 (Subject of Investigation/LOI)	G [auth H]	N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide C22 H28 N2 O PJMPHNIQZUBGLI-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 0.316 
• R-Value Work: 0.278 
• R-Value Observed: 0.297 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.635	α = 90
b = 114.635	β = 90
c = 90.951	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): McGovern, M.R., Rodarte, J.V., Pancera, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	UG3 DA047711

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Structure summary