8S6T: Fab-3F1 complexed to a bis-STn glycopeptide

Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide. Determined by X-ray diffraction at 1.85 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 1.85 Å
Organisms: Mus musculus, synthetic construct
Chains: 3
Atoms: 3,517
Mol. weight: 48.57 kDa
Released: 25 Jun 2025

Explore 8S6T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8S6T contains 19 α-helices and 43 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: 10 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
α-helix	33	1
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	103	1	2
β-strand	107-111	5	2
α-helix	114-116	3
β-strand	117	1	3
α-helix	118-119	2
β-strand	120-124	5	4
β-strand	135-145	11	4
β-strand	146	1	3
β-strand	151-154	4	5
α-helix	155-157	3
β-strand	159	1	5
β-strand	163-165	3	4
α-helix	166-168	3
β-strand	169-171	3	4
β-strand	174-184	11	4
β-strand	193-199	7	5
α-helix	200-202	3
β-strand	204-210	7	5

Chain B: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
α-helix	43-44	2
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-66	5	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
α-helix	96	1
β-strand	97-98	2	7
β-strand	102-106	5	7
β-strand	111	1	8
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	9
β-strand	140	1	8
β-strand	145-150	6	10
β-strand	153-155	3	10
β-strand	159-163	5	9
α-helix	164-167	4
β-strand	173-182	10	9
α-helix	183-186	4
β-strand	191-197	7	10
α-helix	204	1
β-strand	205-210	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3F1 (vh-VH1)	A	protein	215	Mus musculus
3F1 (vl-cl)	B	protein	211	Mus musculus
Mucin-1 subunit beta	C	protein	13	synthetic construct	P15941 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8S6T_1 3F1 (VH-VH1) (chains A)
QVQLKQSDAELVKPGASVKISCKASGYTFTDHAIHWVKQKPEQGLDWIGYISPGNGDIKY
NEKFKDKVTLTADKSSSTASMHLNSLTSEDSAVYFCKRSLLALDYWGQGTTLTVSSAKTT
PPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTL
SSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Sequence of entity 2 (B), FASTA

>8S6T_2 3F1 (VL-CL) (chains B)
DILMTQSHKFMSTSVGDRVSITCKASQDVGTNIAWYQQKPGRSPKVLIYSASTRHTGVPD
RFTGSGSGTDFTLTISNVQSEDLTDYFCQQYSSFPLTFGVGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Sequence of entity 3 (C), FASTA

>8S6T_3 Mucin-1 subunit beta (chains C)
PAPGSTAPPAHGV

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
8S6K 1.75 Å, Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide
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…
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

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