SMTL ID : 8s6t.1

Crystal structure of Fab-3F1 complexed to a bis-STn glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x A2G- SIA: N-acetyl-alpha-neuraminic acid-(2-6)-2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G-SIA.1: 10 residues within 4Å: Chain A: T.30, D.31, A.33, S.52, G.54, N.55, D.57, K.59 Chain C: T.6 Ligands: A2G-SIA.2 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:S.52, A:S.52, A:N.55, A:D.57, A:D.57 Water bridges: C:S.5, C:T.6, C:T.6 Salt bridges: A:K.59 A2G-SIA.2: 15 residues within 4Å: Chain A: D.31, H.32, A.33, H.35, Y.50, R.98, S.99, L.100, L.101, A.102, L.103, Y.105 Chain B: Y.49 Chain C: S.5 Ligands: A2G-SIA.1 7 PLIP interactions: 4 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:Y.50, B:Y.49 Hydrogen bonds: A:D.31, A:A.33, A:H.35, A:L.100, C:S.5, C:S.5, A:R.98, A:S.99, A:A.102 Salt bridges: A:H.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hurtado-Guerrero, R. et al., Recognizing Tn and STn Epitopes in Protein Context: Structural Advances in Phage Display Libraries for Tumor-Specific Antibody Discovery. Nat.Chem.Biol. (2025)

Release Date

2025-06-25

Peptides

3F1 (VH-VH1): A
3F1 (VL-CL): B
Mucin-1 subunit beta: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

3F1 (VH-VH1)

3F1 (VL-CL)

Mucin-1 subunit beta