9GFL | pdb_00009gfl

Crystal structure of ASO binding Fab fragment

PDB DOI: https://doi.org/10.2210/pdb9GFL/pdb

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

Deposited: 2024-08-09 Released: 2025-08-20
Deposition Author(s): Hsia, H.-E., Zanini, C., Simonneau, C., Fraidling, J., Kraft, T., Mayer, K., Sommer, A., Indlekofer, A., Wirth, T., Benz, J., Georges, G., Langer, L.M., Gassner, C., Larraillet, V., Manso, M., Ravn, J., Hofer, K., Emrich, T., Niewoehner, J., Schumacher, F., Brinkmann, U.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.248 (Depositor), 0.235 (DCC)
R-Value Work:
0.209 (Depositor), 0.200 (DCC)
R-Value Observed:
0.211 (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

Improved Targeted Delivery of Antisense Oligonucleotide Conjugates with the Antibody Mask

Hsia, H.-E., Zanini, C., Simonneau, C., Fraidling, J., Kraft, T., Mayer, K., Sommer, A., Indlekofer, A., Wirth, T., Benz, J., Georges, G., Langer, L.M., Gassner, C., Larraillet, V., Manso, M., Ravn, J., Hofer, K., Emrich, T., Niewoehner, J., Schumacher, F., Brinkmann, U.

To be published.

Macromolecule Content

Total Structure Weight: 48.38 kDa
Atom Count: 3,701
Modeled Residue Count: 427
Deposited Residue Count: 445
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment heavy chain	A [auth H]	226	Homo sapiens	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
Fab fragment light chain	B [auth L]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain F [auth H] SDF format, chain H [auth L] MOL2 format, chain F [auth H] MOL2 format, chain H [auth L] mmCIF format, chain F [auth H] mmCIF format, chain H [auth L]	F [auth H], H [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth H] Focus chain H [auth L] Interactions & Density Focus chain F [auth H] Focus chain H [auth L]
EDO Query on EDO 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 I [auth L] MOL2 format, chain C [auth H] MOL2 format, chain D [auth H] MOL2 format, chain E [auth H] MOL2 format, chain I [auth L] mmCIF format, chain C [auth H] mmCIF format, chain D [auth H] mmCIF format, chain E [auth H] mmCIF format, chain I [auth L]	C [auth H], D [auth H], E [auth H], I [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain I [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain I [auth L]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth H] Interactions & Density Focus chain G [auth H]