SMTL ID : 8s6k.1 (1 other biounit)

Crystal structure of ScFv-G2D11 complexed to a bis-Tn glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- GLY- SER- THR- ALA- PRO- NH2: Mucin-1 subunit alpha(Non-covalent)

ALA-PRO-GLY-SER-THR-ALA-PRO-NH2.1: 9 residues within 4Å: Chain A: D.31, L.100, A.166, W.184, Y.225, S.226, Y.228 Ligands: A2G.9, A2G.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.166, A:W.184, A:Y.228

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 8 residues within 4Å: Chain A: H.35, W.47, K.97, S.99, P.101, Y.170, Q.223, L.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.170, A:Q.223 EDO.3: 6 residues within 4Å: Chain A: K.38, R.39, K.40, G.44, L.45, E.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.38, A:K.38, A:K.40, A:G.44 EDO.4: 5 residues within 4Å: Chain A: Y.60, F.64, K.65, G.66, A.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.64, A:G.66 EDO.5: 3 residues within 4Å: Chain A: I.58, Y.60, K.65 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.58, A:K.65, A:K.65 Water bridges: A:I.58 EDO.6: 4 residues within 4Å: Chain A: Y.50, D.57, I.58, K.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.50, A:I.58 Water bridges: A:Y.60 EDO.7: 2 residues within 4Å: Chain A: F.144, E.239 No protein-ligand interaction detected (PLIP) EDO.8: 3 residues within 4Å: Chain A: G.150, N.211, Q.213 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.211, A:Q.213 Water bridges: A:V.149

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

A2G.9: 12 residues within 4Å: Chain A: D.31, H.32, A.33, H.35, Y.50, S.99, L.100, F.104, Y.228 Ligands: ALA-PRO-GLY-SER-THR-ALA-PRO-NH2.1, ALA-PRO-GLY-SER-THR-ALA-PRO-NH2.1, A2G.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.50 Hydrogen bonds: A:D.31, A:H.32, A:A.33 Water bridges: A:S.99, A:S.99 A2G.10: 9 residues within 4Å: Chain A: D.31, A.33, S.52, N.55, D.57 Ligands: ALA-PRO-GLY-SER-THR-ALA-PRO-NH2.1, ALA-PRO-GLY-SER-THR-ALA-PRO-NH2.1, ALA-PRO-GLY-SER-THR-ALA-PRO-NH2.1, A2G.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.52, A:S.52, A:N.55

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

ScFv-G2D11: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ScFv-G2D11

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