SMTL ID : 8axh.1

Crystal structure of a MUC1-like glycopeptide containing the unnatural L-4-hydroxynorvaline in complex with scFv-SM3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- VAH- ARG- PRO- NH2: Mucin-1 subunit alpha(Non-covalent)

ALA-PRO-ASP-VAH-ARG-PRO-NH2.1: 9 residues within 4Å: Chain A: N.31, Y.32, W.33, Q.103, Y.168, W.227, W.232 Ligands: A2G.7, EDO.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.33, A:Y.168, A:Y.168, A:Y.168, A:W.227, A:W.232 Hydrogen bonds: A:Y.32, A:Y.32, A:W.33, A:Q.103 Water bridges: A:W.33, A:R.52, A:G.102, A:W.227

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

EDO.2: 5 residues within 4Å: Chain A: V.2, Q.3, L.4, W.107, Q.109 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.2, A:L.4, A:Q.109, A:Q.109 EDO.3: 3 residues within 4Å: Chain A: Q.13, P.14, S.116 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.116 EDO.4: 6 residues within 4Å: Chain A: E.174, K.175, P.176, D.177, H.178, I.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.175, A:H.178 EDO.5: 3 residues within 4Å: Chain A: T.146, S.147, E.150 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.146, A:S.147 Water bridges: A:T.145 EDO.6: 2 residues within 4Å: Chain A: V.152, T.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.153 EDO.8: 7 residues within 4Å: Chain A: G.102, Q.103, G.186, N.189 Ligands: ALA-PRO-ASP-VAH-ARG-PRO-NH2.1, ALA-PRO-ASP-VAH-ARG-PRO-NH2.1, ALA-PRO-ASP-VAH-ARG-PRO-NH2.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.103, A:Q.103, A:N.189 Water bridges: A:G.102

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

A2G.7: 4 residues within 4Å: Chain A: W.33 Ligands: ALA-PRO-ASP-VAH-ARG-PRO-NH2.1, ALA-PRO-ASP-VAH-ARG-PRO-NH2.1, ALA-PRO-ASP-VAH-ARG-PRO-NH2.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bermejo, I.A. et al., Structure-Guided Approach for the Development of MUC1-Glycopeptide-Based Cancer Vaccines with Predictable Responses. Jacs Au (2024)

Release Date

2023-08-09

Peptides

Single-chain variable antibody (scFv) SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

Single-chain variable antibody (scFv) SM3

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