9GFD | pdb_00009gfd

Crystal structure of ASO binding Fab fragment with ASO139

PDB DOI: https://doi.org/10.2210/pdb9GFD/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., Geroges, G., Langer, M.L., 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: 1.43 Å
R-Value Free:
0.205 (Depositor), 0.205 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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., Geroges, G., Langer, M.L., 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: 49.44 kDa
Atom Count: 3,844
Modeled Residue Count: 433
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
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
A1IKZ (Subject of Investigation/LOI) Query on A1IKZ Download Ideal Coordinates CCD File SDF format, chain J [auth L] MOL2 format, chain J [auth L] mmCIF format, chain J [auth L]	J [auth L]	1-[(1~{S},3~{R},4~{R},7~{S})-7-[[(1~{R},3~{R},4~{R},7~{S})-7-[[(1~{R},3~{R},4~{R},7~{S})-3-(6-aminopurin-9-yl)-7-[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-3-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-2,5-dioxabicyclo[2.2.1]heptan-1-yl]methoxy-sulfanyl-phosphoryl]oxy-1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-3-yl]-5-methyl-pyrimidine-2,4-dione C₄₂ H₅₂ N₁₃ O₂₂ P₃ S₃ YGGSNWRUJSQEEQ-LYYFKHMFSA-N		Interactions Focus chain J [auth L] Interactions & Density Focus chain J [auth L]
HIS Query on HIS Download Ideal Coordinates CCD File SDF format, chain G [auth L] MOL2 format, chain G [auth L] mmCIF format, chain G [auth L]	G [auth L]	HISTIDINE C₆ H₁₀ N₃ O₂ HNDVDQJCIGZPNO-YFKPBYRVSA-O		Interactions Focus chain G [auth L] Interactions & Density Focus chain G [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 F [auth L] SDF format, chain H [auth L] 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 F [auth L] MOL2 format, chain H [auth L] 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 F [auth L] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L]	C [auth H] D [auth H] E [auth H] F [auth L] H [auth L] C [auth H], D [auth H], E [auth H], F [auth L], H [auth L], 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 F [auth L] Focus chain H [auth L] Focus chain I [auth L] Interactions & Density Focus chain C [auth H] Focus chain D [auth H] Focus chain E [auth H] Focus chain F [auth L] Focus chain H [auth L] Focus chain I [auth L]