9AXO

Crystal Structure of Antibody HY11-7E1_Ch2 Fab in Complex with Fentanyl

PDB DOI: https://doi.org/10.2210/pdb9AXO/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.278
R-Value Work: 0.232
R-Value Observed: 0.234

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

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

Rodarte, J.V., Pravetoni, M.

To be published.

Macromolecule Content

Total Structure Weight: 50.19 kDa
Atom Count: 3,541
Modelled Residue Count: 434
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HY11-7E1_Ch2 Fab Heavy Chain	A [auth H]	232	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HY11-7E1_Ch2 Fab Light Chain	B [auth L]	213	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7V7 (Subject of Investigation/LOI) Query on 7V7 Download Ideal Coordinates CCD File SDF format, chain M [auth L] MOL2 format, chain M [auth L] mmCIF format, chain M [auth L]	M [auth L]	N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide C₂₂ H₂₈ N₂ O PJMPHNIQZUBGLI-UHFFFAOYSA-N		Interactions Focus chain M [auth L] Interactions & Density Focus chain M [auth L]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth H] SDF format, chain D [auth H] SDF format, chain E [auth H] SDF format, chain F [auth H] SDF format, chain G [auth H] SDF format, chain H SDF format, chain I [auth H] SDF format, chain J [auth H] SDF format, chain K [auth H] SDF format, chain L [auth H] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain P [auth L] SDF format, chain Q [auth L] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain F [auth H] MOL2 format, chain G [auth H] MOL2 format, chain H MOL2 format, chain I [auth H] MOL2 format, chain J [auth H] MOL2 format, chain K [auth H] MOL2 format, chain L [auth H] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain F [auth H] mmCIF format, chain G [auth H] mmCIF format, chain H mmCIF format, chain I [auth H] mmCIF format, chain J [auth H] mmCIF format, chain K [auth H] mmCIF format, chain L [auth H] mmCIF format, chain N [auth L] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L] mmCIF format, chain Q [auth L]	C [auth H] D [auth H] E [auth H] F [auth H] G [auth H] C [auth H], D [auth H], E [auth H], F [auth H], G [auth H], H, I [auth H], J [auth H], K [auth H], L [auth H], N [auth L], O [auth L], P [auth L], Q [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain I [auth H] Focus chain J [auth H] Focus chain K [auth H] Focus chain L [auth H] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L]