8S6K: ScFv-G2D11 complexed to a bis-Tn glycopeptide

Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide. Determined by X-ray diffraction at 1.75 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 1.75 Å
Organisms: Mus musculus, Homo sapiens
Chains: 4
Atoms: 4,213
Mol. weight: 56.69 kDa
Ligands: A2G
Released: 25 Jun 2025

Explore 8S6K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S6K contains 17 α-helices and 44 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-52	8	2
β-strand	56A-59	4	2
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	102-103	2	2
β-strand	107-111	5	2
α-helix	1002-1003	2
β-strand	1004-1005	2	3
β-strand	1010-1013	4	2
β-strand	1019-1025	7	3
β-strand	1033-1038	6	2
β-strand	1045-1049	5	2
β-strand	1053-1054	2	2
α-helix	1055	1
β-strand	1062-1067	6	3
β-strand	1070-1075	6	3
α-helix	1080-1082	3
β-strand	1084-1090	7	2
α-helix	1096	1
β-strand	1097-1098	2	2
β-strand	1102-1106	5	2

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	4
α-helix	7-9	3
β-strand	10-12	3	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	34-39	6	5
β-strand	45-52	8	5
β-strand	56A-59	4	5
α-helix	61-63	3
β-strand	67-72	6	4
α-helix	73-75	3
β-strand	77-82	6	4
α-helix	84-86	3
β-strand	88-94	7	5
β-strand	102-103	2	5
β-strand	107-111	5	5
α-helix	1002-1003	2
β-strand	1004-1005	2	6
β-strand	1010-1013	4	5
β-strand	1019-1025	7	6
β-strand	1033-1038	6	5
β-strand	1045-1049	5	5
β-strand	1053-1054	2	5
α-helix	1055	1
β-strand	1062-1067	6	6
β-strand	1070-1075	6	6
α-helix	1080-1082	3
β-strand	1084-1090	7	5
α-helix	1096	1
β-strand	1097-1098	2	5
β-strand	1102-1106	5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ScFv-G2D11	A, H	protein	250	Mus musculus
Mucin-1 subunit alpha	M, N	protein	8	Homo sapiens	P15941 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>8S6K_1 ScFv-G2D11 (chains A, H)
QVQLQQSDAELVKPGASVKISCKASGYIFADHAIHWVKRKPEQGLEWIGYISPGNDDIKY
NEKFKGKATLTADKSSSTAYMQLNSLTSEDSAVYFCKRSLPGTFDYWGQGTTLTVSSSSG
GGGSGGGGGSSGSSDVVMTQSHKFMSTSVGDRVSITCKASQDVGTAVAWYQQKPGQSPKL
LIYWASTRHTGVPDRFTGSGSGTDFTLTISNVQSEDLADYFCQQYSSYPLTFGGGTKLEM
KRGGHHHHHH

Sequence of entity 2 (M, N), FASTA

>8S6K_2 Mucin-1 subunit alpha (chains M, N)
APGSTAPX

Ligands and cofactors

ID	Name	Formula	Copies
A2G	2-acetamido-2-deoxy-alpha-D-galactopyranose	C8 H15 N O6	4

Water and common crystallization additives (EDO) are not listed.

Primary citation

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. et al. Nat Chem Biol (2025).

Other PDB entries of the same protein (UniProt P15941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BSC 1.3 Å, Crystal structure of the Mucin-1 SEA domain
7V64 1.56 Å, Crystal structure of Antibody 16A in complex with MUC1 Glycopeptide(GlycoT)
6BSB 1.6 Å, Crystal structure of the Mucin-1 SEA domain, L1105M mutant, Selenium-derivative
6FZQ 1.7 Å, Crystal structure of scFv-SM3 in complex with compound 3
6KX1 1.77 Å, Crystal structure of SN-101 mAb in complex with MUC1 glycopeptide
6FZR 1.8 Å, Crystal structure of scFv-SM3 in complex with compound 2
8AXH 1.85 Å, Crystal structure of a MUC1-like glycopeptide containing the unnatural…
8S6T 1.85 Å, Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide
1SM3 1.95 Å, Crystal structure of the tumor specific antibody SM3 complex with its peptide epitope
8S6V 1.95 Å, Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide
5T6P 1.97 Å, Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide
6TGG 2.0 Å, scFv-1SM3 in complex with glycopeptide containing an sp2-imino sugar

Browse structure collections

About this viewer

MolViewer shows 8S6K directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.