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

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3F1 (VH-VH1)	A	215	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3F1 (VL-CL)	B	211	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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	3D 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

View Full Validation Report

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

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.