8S6K | pdb_00008s6k

Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide

PDB DOI: https://doi.org/10.2210/pdb8S6K/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2024-02-27 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: 1.75 Å
R-Value Free:
0.221 (Depositor), 0.229 (DCC)
R-Value Work:
0.182 (Depositor), 0.191 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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: 56.69 kDa
Atom Count: 4,213
Modeled Residue Count: 481
Deposited Residue Count: 516
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ScFv-G2D11	A, B [auth H]	250	Mus musculus	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-1 subunit alpha	C [auth M], D [auth N]	8	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P15941 (Homo sapiens) Explore P15941 Go to UniProtKB: P15941
PHAROS: P15941 GTEx: ENSG00000185499
Entity Groups
UniProt Group	P15941
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C [auth M] Focus chain D [auth N]	Go to GlyGen: P15941-1
Sequence Annotations Expand
Reference Sequence

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 Q [auth M] SDF format, chain R [auth M] SDF format, chain S [auth N] SDF format, chain T [auth N] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain S [auth N] mmCIF format, chain T [auth N]	Q [auth M], R [auth M], S [auth N], T [auth N]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth N] Focus chain T [auth N] Interactions & Density Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth N] Focus chain T [auth N]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] SDF format, chain O [auth H] SDF format, chain P [auth H] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [auth H] mmCIF format, chain O [auth H] mmCIF format, chain P [auth H]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth H], M [auth H], N [auth H], O [auth H], P [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Focus chain O [auth H] Focus chain P [auth H]