SMTL ID : 8s73.2 (1 other biounit)

Crystal structure of Fab-antiCD43 monoclonal antibody complexed to a bis-Tn glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GLY- ALA- SER- THR- GLY- SER- PRO: bis-Tn glycopeptide(Non-covalent)

GLY-ALA-SER-THR-GLY-SER-PRO.1: 6 residues within 4Å: Chain B: Y.35, Y.95, G.96, Y.99 Ligands: A2G.3, A2G.4 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.35, B:Y.35

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: F.170, P.171, T.180, L.181, S.182 Chain B: L.163, S.165, S.179, S.180, T.181 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.165, B:S.179, B:S.179, B:T.181, A:P.171, A:S.182

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.3: 10 residues within 4Å: Chain A: A.30, D.31, A.33, Y.50, S.52, N.55, D.57 Ligands: GLY-ALA-SER-THR-GLY-SER-PRO.1, GLY-ALA-SER-THR-GLY-SER-PRO.1, A2G.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.50, A:S.52, A:S.52, A:N.55, A:D.57 A2G.4: 11 residues within 4Å: Chain A: D.31, H.32, A.33, H.35, Y.50, S.99, L.100, F.104 Chain B: Y.99 Ligands: GLY-ALA-SER-THR-GLY-SER-PRO.1, A2G.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.50 Hydrogen bonds: A:H.32, A:A.33

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

G2D11(VH-CH1): A
antiCD43(VL-CL): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

G2D11(VH-CH1)

antiCD43(VL-CL)

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