9AXN

Crystal Structure of Anti-Fentanyl Antibody HY11-6B2_Mu Fab in Complex with Fentanyl

PDB DOI: https://doi.org/10.2210/pdb9AXN/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: 2.40 Å
R-Value Free: 0.263
R-Value Work: 0.224
R-Value Observed: 0.226

Starting Models: 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: 389.83 kDa
Atom Count: 27,064
Modelled Residue Count: 3,388
Deposited Residue Count: 3,536
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HY11-6B2_Mu Fab Heavy Chain	A [auth H] C [auth A] D [auth C] G [auth E] J [auth I] A [auth H], C [auth A], D [auth C], G [auth E], J [auth I], K [auth M], M [auth O], O [auth Q]	228	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
HY11-6B2_Mu Fab Light Chain	B [auth L] E [auth D] F [auth B] H [auth F] I [auth J] B [auth L], E [auth D], F [auth B], H [auth F], I [auth J], L [auth N], N [auth P], P [auth R]	214	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 DB [auth O] SDF format, chain GA [auth E] SDF format, chain IB [auth R] SDF format, chain Q [auth H] SDF format, chain SA [auth I] SDF format, chain UA [auth M] SDF format, chain W [auth A] SDF format, chain Y [auth C] MOL2 format, chain DB [auth O] MOL2 format, chain GA [auth E] MOL2 format, chain IB [auth R] MOL2 format, chain Q [auth H] MOL2 format, chain SA [auth I] MOL2 format, chain UA [auth M] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth C] mmCIF format, chain DB [auth O] mmCIF format, chain GA [auth E] mmCIF format, chain IB [auth R] mmCIF format, chain Q [auth H] mmCIF format, chain SA [auth I] mmCIF format, chain UA [auth M] mmCIF format, chain W [auth A] mmCIF format, chain Y [auth C]	DB [auth O] GA [auth E] IB [auth R] Q [auth H] SA [auth I] DB [auth O], GA [auth E], IB [auth R], Q [auth H], SA [auth I], UA [auth M], W [auth A], Y [auth C]	N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide C₂₂ H₂₈ N₂ O PJMPHNIQZUBGLI-UHFFFAOYSA-N		Interactions Focus chain DB [auth O] Focus chain GA [auth E] Focus chain IB [auth R] Focus chain Q [auth H] Focus chain SA [auth I] Focus chain UA [auth M] Focus chain W [auth A] Focus chain Y [auth C] Interactions & Density Focus chain DB [auth O] Focus chain GA [auth E] Focus chain IB [auth R] Focus chain Q [auth H] Focus chain SA [auth I] Focus chain UA [auth M] Focus chain W [auth A] Focus chain Y [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth B] SDF format, chain EB [auth O] SDF format, chain FB [auth P] SDF format, chain GB [auth Q] SDF format, chain HA [auth E] SDF format, chain LA [auth F] SDF format, chain NA [auth J] SDF format, chain OA [auth J] SDF format, chain R [auth H] SDF format, chain S [auth L] SDF format, chain T [auth L] SDF format, chain TA [auth I] SDF format, chain VA [auth M] SDF format, chain WA [auth M] SDF format, chain X [auth A] SDF format, chain XA [auth N] SDF format, chain YA [auth N] SDF format, chain Z [auth C] SDF format, chain ZA [auth N] SDF format, chain MA [auth F] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth O] MOL2 format, chain FB [auth P] MOL2 format, chain GB [auth Q] MOL2 format, chain HA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain NA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain R [auth H] MOL2 format, chain S [auth L] MOL2 format, chain T [auth L] MOL2 format, chain TA [auth I] MOL2 format, chain VA [auth M] MOL2 format, chain WA [auth M] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth N] MOL2 format, chain YA [auth N] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth N] MOL2 format, chain MA [auth F] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth O] mmCIF format, chain FB [auth P] mmCIF format, chain GB [auth Q] mmCIF format, chain HA [auth E] mmCIF format, chain LA [auth F] mmCIF format, chain NA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain R [auth H] mmCIF format, chain S [auth L] mmCIF format, chain T [auth L] mmCIF format, chain TA [auth I] mmCIF format, chain VA [auth M] mmCIF format, chain WA [auth M] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth N] mmCIF format, chain YA [auth N] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth N] mmCIF format, chain MA [auth F]	BA [auth D] CA [auth D] DA [auth D] EA [auth B] EB [auth O] BA [auth D], CA [auth D], DA [auth D], EA [auth B], EB [auth O], FB [auth P], GB [auth Q], HA [auth E], LA [auth F], MA [auth F], NA [auth J], OA [auth J], R [auth H], S [auth L], T [auth L], TA [auth I], VA [auth M], WA [auth M], X [auth A], XA [auth N], YA [auth N], Z [auth C], ZA [auth N]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth B] Focus chain EB [auth O] Focus chain FB [auth P] Focus chain GB [auth Q] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain R [auth H] Focus chain S [auth L] Focus chain T [auth L] Focus chain TA [auth I] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain X [auth A] Focus chain XA [auth N] Focus chain YA [auth N] Focus chain Z [auth C] Focus chain ZA [auth N] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth B] Focus chain EB [auth O] Focus chain FB [auth P] Focus chain GB [auth Q] Focus chain HA [auth E] Focus chain LA [auth F] Focus chain MA [auth F] Focus chain NA [auth J] Focus chain OA [auth J] Focus chain R [auth H] Focus chain S [auth L] Focus chain T [auth L] Focus chain TA [auth I] Focus chain VA [auth M] Focus chain WA [auth M] Focus chain X [auth A] Focus chain XA [auth N] Focus chain YA [auth N] Focus chain Z [auth C] Focus chain ZA [auth N]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain AB [auth N] SDF format, chain BB [auth N] SDF format, chain HB [auth Q] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain PA [auth J] SDF format, chain QA [auth J] SDF format, chain RA [auth J] SDF format, chain U [auth L] SDF format, chain V [auth L] SDF format, chain CB [auth N] MOL2 format, chain AB [auth N] MOL2 format, chain BB [auth N] MOL2 format, chain HB [auth Q] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth J] MOL2 format, chain RA [auth J] MOL2 format, chain U [auth L] MOL2 format, chain V [auth L] MOL2 format, chain CB [auth N] mmCIF format, chain AB [auth N] mmCIF format, chain BB [auth N] mmCIF format, chain HB [auth Q] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain PA [auth J] mmCIF format, chain QA [auth J] mmCIF format, chain RA [auth J] mmCIF format, chain U [auth L] mmCIF format, chain V [auth L] mmCIF format, chain CB [auth N]	AB [auth N] BB [auth N] CB [auth N] HB [auth Q] IA [auth E] AB [auth N], BB [auth N], CB [auth N], HB [auth Q], IA [auth E], JA [auth E], KA [auth E], PA [auth J], QA [auth J], RA [auth J], U [auth L], V [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain HB [auth Q] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain U [auth L] Focus chain V [auth L] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain HB [auth Q] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain RA [auth J] Focus chain U [auth L] Focus chain V [auth L]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain FA [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain FA [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain FA [auth B]	AA [auth C], FA [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain FA [auth B] Interactions & Density Focus chain AA [auth C] Focus chain FA [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A [auth H] C [auth A] D [auth C] G [auth E] J [auth I] A [auth H], C [auth A], D [auth C], G [auth E], J [auth I], K [auth M], M [auth O], O [auth Q]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN