8S6T | pdb_00008s6t

Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide

PDB DOI: https://doi.org/10.2210/pdb8S6T/pdb

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

Deposited: 2024-02-28 Released: 2025-06-25
Deposition Author(s): Hurtado-Guerrero, R., Gines, I.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.267 (Depositor), 0.274 (DCC)
R-Value Work:
0.230 (Depositor), 0.237 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8S6T

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: 48.57 kDa
Atom Count: 3,517
Modeled Residue Count: 428
Deposited Residue Count: 439
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3F1 (VH-VH1)	A	215	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3F1 (VL-CL)	B	211	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-1 subunit beta	C	13	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens) Explore P15941 Go to UniProtKB: P15941
PHAROS: P15941 GTEx: ENSG00000185499
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15941
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C	Go to GlyGen: P15941-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose	D, E	2		O-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G36123IU GlyCosmos: G36123IU GlyGen: G36123IU

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.267 (Depositor), 0.274 (DCC)
R-Value Work: 0.230 (Depositor), 0.237 (DCC)
R-Value Observed: 0.231 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.779	α = 90
b = 74.779	β = 90
c = 392.355	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Hurtado-Guerrero, R.

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.