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
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wwPDB Validation 3D Report Full Report

Validation slider image for 8S73

Ligand Structure Quality Assessment

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

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

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

Find similar proteins by:

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

Find similar proteins by:

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

Find similar proteins by: Sequence | 3D Structure

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G (Subject of Investigation/LOI) Query on A2G Download:Ideal Coordinates CCD File SDF format, chain L [auth N] SDF format, chain K [auth N] SDF format, chain J [auth M] SDF format, chain I [auth M] MOL2 format, chain L [auth N] MOL2 format, chain K [auth N] MOL2 format, chain J [auth M] MOL2 format, chain I [auth M] mmCIF format, chain L [auth N] mmCIF format, chain K [auth N] mmCIF format, chain J [auth M] mmCIF format, chain I [auth M]	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		Interactions Focus chain I [auth M] Focus chain J [auth M] Focus chain K [auth N] Focus chain L [auth N] Interactions & Density Focus chain I [auth M] Focus chain J [auth M] Focus chain K [auth N] Focus chain L [auth N]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth B]	G [auth B], H [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Focus chain H [auth D] Interactions & Density Focus chain G [auth B] Focus chain H [auth D]

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

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Ligand Structure Quality Assessment

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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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.