9R2E | pdb_00009r2e

Structure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1

PDB DOI: https://doi.org/10.2210/pdb9R2E/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Homo sapiens
Mutation(s): No

Deposited: 2025-04-30 Released: 2025-05-14
Deposition Author(s): Pannecoucke, E., Voet, S., Deweirdt, L., Verbeiren, J., Gabriels, S., Provost, M., Freier, R., Koenig, J., Lammens, A., Silence, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free:
0.252 (Depositor), 0.250 (DCC)
R-Value Work:
0.211 (Depositor), 0.209 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of ARGX-121 Fab fragment in complex with the Fc fragment of IgA1

Voet, S., Provost, M., Deweirdt, L., Verbeiren, J., Gabriels, S., Silence, K., Pannecoucke, E.

To be published.

Macromolecule Content

Total Structure Weight: 148.42 kDa
Atom Count: 10,097
Modeled Residue Count: 1,283
Deposited Residue Count: 1,384
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARGX-121 Fab fragment heavy chain	A [auth H], E [auth A]	244	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ARGX-121 Fab fragment light chain	B [auth L], F [auth B]	235	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 1 of Immunoglobulin heavy constant alpha 1	C [auth P], D [auth Q]	213	Homo sapiens	Mutation(s): 0 Gene Names: IGHA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01876 (Homo sapiens) Explore P01876 Go to UniProtKB: P01876
PHAROS: P01876 GTEx: ENSG00000211895
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01876
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain J [auth L] SDF format, chain I [auth H] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth L] MOL2 format, chain I [auth H] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth L] mmCIF format, chain I [auth H]	I [auth H], J [auth L], M [auth A], O [auth A], P [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain J [auth L] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain I [auth H] Focus chain J [auth L] Focus chain M [auth A] Focus chain O [auth A] Focus chain P [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain N [auth A] SDF format, chain H SDF format, chain G [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain N [auth A] MOL2 format, chain H MOL2 format, chain G [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain N [auth A] mmCIF format, chain H mmCIF format, chain G [auth H]	G [auth H], H, N [auth A], Q [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Focus chain H Focus chain N [auth A] Focus chain Q [auth A] Interactions & Density Focus chain G [auth H] Focus chain H Focus chain N [auth A] Focus chain Q [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain L [auth P] SDF format, chain K [auth L] MOL2 format, chain R [auth B] MOL2 format, chain L [auth P] MOL2 format, chain K [auth L] mmCIF format, chain R [auth B] mmCIF format, chain L [auth P] mmCIF format, chain K [auth L]	K [auth L], L [auth P], R [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth L] Focus chain L [auth P] Focus chain R [auth B] Interactions & Density Focus chain K [auth L] Focus chain L [auth P] Focus chain R [auth B]