9GF5 | pdb_00009gf5

CRYSTAL STRUCTURE OF COMPLEX OF ASO BINDING FAB FRAGMENT IN COMPLEX WITH ASO980

• PDB DOI: https://doi.org/10.2210/pdb9GF5/pdb

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


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.217 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Improved Targeted Delivery of Antisense Oligonucleotide Conjugates with the Antibody Mask

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.37 kDa 
• Atom Count: 3,921 
• Modeled Residue Count: 427 
• Deposited Residue Count: 445 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ASO Fab fragment heavy chain	A [auth H]	226	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ASO Fab fragment light chain	B [auth L]	219	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IKQ (Subject of Investigation/LOI)	H [auth L]	1-[(2R,4S,5R)-4-[[(1R,3R,4R,7S)-7-[[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-[[(2R,3S,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl]oxy-oxolan-2-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-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione C40 H52 N13 O20 P3 S3 LASMOYDWHKUTQQ-CXQZBYKISA-N
EPE	G [auth L]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	E [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	C [auth H], D [auth H], F [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.217 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.615	α = 90
b = 59.604	β = 94.34
c = 62.508	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SADABS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-08-20 
Deposition Author(s): Hung-En, H., Zanini, C., Simonneau, C., Fraidling, J., Kraft, T., Mayer, K., Sommer, A., Indlekofer, A., Wirth, T., Benz, J., Georges, G., Langer, M., Gassner, C., Larraillet, V., Manso, M., Ravn, J., Hofer, K., Emrich, T., Niewoehner, J., Schumacher, F., Brinkmann, U.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-20
  Type: Initial release