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
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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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ScFv-G2D11	A, B [auth H]	250	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: 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 T [auth N] SDF format, chain S [auth N] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain T [auth N] MOL2 format, chain S [auth N] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain T [auth N] mmCIF format, chain S [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 K [auth A] SDF format, chain O [auth H] SDF format, chain J [auth A] SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [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 K [auth A] MOL2 format, chain O [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [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 K [auth A] mmCIF format, chain O [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth H] mmCIF format, chain M [auth H] mmCIF format, chain N [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]