9AXP

Crystal Structure of HY11-7E1_Hu3 Fab in Complex with Carfentanil

• PDB DOI: https://doi.org/10.2210/pdb9AXP/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): 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: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 

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 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 96.43 kDa 
• Atom Count: 6,578 
• Modelled Residue Count: 834 
• Deposited Residue Count: 880 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HY11-7E1_Hu3 Fab Heavy Chain	A, C [auth H]	226	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HY11-7E1_Hu3 Fab Light Chain	B, D [auth L]	214	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AH7 (Subject of Investigation/LOI)	F [auth A], H	methyl 1-{3-[(2-aminoethyl)amino]-3-oxopropyl}-4-(N-phenylpropanamido)piperidine-4-carboxylate C21 H32 N4 O4 XXIJBKRNWYCXNY-UHFFFAOYSA-N
ACT	E [auth A], G [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, C [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.231 
• R-Value Observed: 0.233 
• Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.162	α = 90
b = 154.893	β = 90.63
c = 159.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): 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