SMTL ID : 8s6v.1 (1 other biounit)

Crystal structure of Fab-2D9 chimera complexed to a bis-Tn glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: Y.60, F.64, K.65, G.66, K.67, A.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.66, A:K.67, A:A.68, A:A.68 EDO.2: 7 residues within 4Å: Chain A: Y.149, E.152, P.153, V.154, P.171, A.172, L.181 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.149, A:V.154, A:V.154, A:A.172 EDO.4: 8 residues within 4Å: Chain A: H.35, K.97, S.99, L.100, P.101 Chain B: Y.42, Q.95, F.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.35 EDO.5: 1 residues within 4Å: Chain B: K.189 No protein-ligand interaction detected (PLIP)

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: V.2, Y.27, R.98, F.104 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.98 Salt bridges: A:R.98 SO4.6: 4 residues within 4Å: Chain B: E.160, R.161, Q.162, N.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.162, B:N.163, B:N.163 Salt bridges: B:R.161

2 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.7: 9 residues within 4Å: Chain A: D.31, A.33, Y.50, S.52, N.55, D.57 Chain C: S.4, T.5 Ligands: A2G.8 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:Y.50, A:S.52, A:S.52, A:N.55, A:D.57 Water bridges: C:S.4, C:T.5 A2G.8: 10 residues within 4Å: Chain A: D.31, H.32, A.33, H.35, S.99, L.100, F.104 Chain B: Y.100 Chain C: T.5 Ligands: A2G.7 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.100 Hydrogen bonds: A:H.32, A:A.33, C:T.5 Water bridges: A:S.99, A:S.99

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
2D9 (VL-CL): B
Mucin-1 subunit alpha: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
M

G2D11 (VH-CH1)

2D9 (VL-CL)

Mucin-1 subunit alpha

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