8S73 | pdb_00008s73

Crystal structure of Fab-antiCD43 monoclonal antibody complexed to a bis-Tn glycopeptide

• PDB DOI: https://doi.org/10.2210/pdb8S73/pdb

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


• Deposited: 2024-02-29 Released: 2025-06-25 
• Deposition Author(s): Hurtado-Guerrero, R., Macias-Leon, J.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: in silico

Literature

Recognizing Tn and STn Epitopes in Protein Context: Structural Advances in Phage Display Libraries for Tumor-Specific Antibody Discovery

Hurtado-Guerrero, R., Gatos, S., Gines-Alcober, I., Macias-Leon, J., Manuel Gonzalez-Ramirez, A., Kasapoglu, I., Veloz, B., Companon, I., Ghirardello, M., Merino, P., Corzana, F., Blixt, O.

(2025) Nat Chem Biol 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 95.99 kDa 
• Atom Count: 6,742 
• Modeled Residue Count: 854 
• Deposited Residue Count: 874 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
G2D11(VH-CH1)	A, C	216	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antiCD43(VL-CL)	B, D	214	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
bis-Tn glycopeptide	E [auth M], F [auth N]	7	Homo sapiens	Mutation(s): 0
Glycosylation
Glycosylation Sites: 2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A2G (Subject of Investigation/LOI)	I [auth M], J [auth M], K [auth N], L [auth N]	2-acetamido-2-deoxy-alpha-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-CBQIKETKSA-N
GOL	G [auth B], H [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.525	α = 90
b = 100.525	β = 90
c = 194.767	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Hurtado-Guerrero, R., Macias-Leon, J.

---

Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2022-136362NB-I00

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release