SMTL ID : 8hrh.1

SN-131/1B2 anti-MUC1 antibody with a glycopeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-1-1-mer

Ligands

1 x A2G- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose

A2G-GAL-SIA.1: 9 residues within 4Å: Chain A: H.71, S.74, I.76, Y.78 Chain B: N.54 Ligands: N7P.2, THR.4, ARG.5, PRO.12 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.74, A:S.74, B:N.54 Water bridges: A:S.74, B:N.52

1 x N7P: 1-ACETYL-L-PROLINE(Non-covalent)

N7P.2: 4 residues within 4Å: Chain A: N.50 Ligands: A2G-GAL-SIA.1, ASP.3, THR.4 2 PLIP interactions: 2 Ligand-Ligand interactions Hydrophobic interactions: T.4 Hydrogen bonds: T.4

1 x ASP: ASPARTIC ACID(Non-covalent)

ASP.3: 8 residues within 4Å: Chain A: N.50, Y.51, S.118, S.119, G.120, T.121 Ligands: N7P.2, THR.4 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.51 Hydrogen bonds: A:N.50, A:G.52, A:G.120, A:T.121 Water bridges: A:T.121, A:R.122, T.4, T.4

1 x THR: THREONINE(Non-covalent)

THR.4: 8 residues within 4Å: Chain A: G.52, H.71, G.120 Ligands: A2G-GAL-SIA.1, N7P.2, ASP.3, ARG.5, PRO.12 7 PLIP interactions: 1 interactions with chain A, 6 Ligand-Ligand interactions Hydrogen bonds: A:G.120, T.4, R.5 Water bridges: D.3, T.4, T.4, T.4

1 x ARG: ARGININE(Non-covalent)

ARG.5: 15 residues within 4Å: Chain A: H.71, Y.78, S.118, S.119, G.120, G.123, F.124 Chain B: E.58, Y.60, F.113, W.120 Ligands: A2G-GAL-SIA.1, THR.4, ALA.6, PRO.12 8 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.120 Salt bridges: B:E.58 pi-Cation interactions: B:W.120, A:F.124 Hydrogen bonds: A:F.124, T.4 Water bridges: A:H.71, A:S.118

1 x ALA: ALANINE(Non-covalent)

ALA.6: 5 residues within 4Å: Chain A: Y.78 Chain B: H.50 Ligands: ARG.5, PRO.12, LPD.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.78

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 7 residues within 4Å: Chain A: Y.169, E.172, P.173, V.174, A.192, L.201 Ligands: PEG.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.169, A:V.174, A:A.192 Water bridges: A:E.172, A:A.192

7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain A: T.189, F.190, P.191 Ligands: TRS.7 No protein-ligand interaction detected (PLIP) PEG.9: 4 residues within 4Å: Chain A: Q.58, V.112, Q.129 Chain B: Q.62 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.62 Water bridges: B:S.67, A:G.130, A:L.132 PEG.14: 7 residues within 4Å: Chain B: L.61, K.63, K.69, L.71, F.86, E.105, D.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.105, B:D.106 PEG.15: 3 residues within 4Å: Chain A: Y.126 Chain B: F.79, S.80 No protein-ligand interaction detected (PLIP) PEG.16: 2 residues within 4Å: Chain B: T.24, R.43 No protein-ligand interaction detected (PLIP) PEG.17: 5 residues within 4Å: Chain B: L.28, Y.111, G.124, G.125, K.127 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.111 PEG.18: 9 residues within 4Å: Chain A: S.185, G.186, H.188, T.206 Chain B: N.162, D.191, K.193, D.194, T.196 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.162, B:D.194, A:T.206 Water bridges: B:T.196

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 7 residues within 4Å: Chain A: I.67, G.68, H.79, N.80, F.83, R.84, A.87 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.67, A:N.80, A:F.83, A:A.87 Water bridges: A:G.85 GOL.11: 3 residues within 4Å: Chain A: Q.24, S.26, K.42 No protein-ligand interaction detected (PLIP)

1 x PRO: PROLINE(Non-covalent)

PRO.12: 10 residues within 4Å: Chain A: Y.78 Chain B: H.50, N.52, Y.56, W.120 Ligands: A2G-GAL-SIA.1, THR.4, ARG.5, ALA.6, LPD.13 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.56

1 x LPD: L-PROLINAMIDE(Non-covalent)

LPD.13: 7 residues within 4Å: Chain A: Y.78 Chain B: S.116, H.117, G.118, W.120 Ligands: ALA.6, PRO.12 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.78 Hydrogen bonds: B:G.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wakui, H. et al., Structural and molecular insight into antibody recognition of dynamic neoepitopes in membrane tethered MUC1 of pancreatic cancer cells and secreted exosomes. Rsc Chem Biol (2023)

Release Date

2023-08-30

Peptides

Heavy chain of SN-131/1B2 antibody Fab: A
Light chain of SN-131/1B2 antibody Fab: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Heavy chain of SN-131/1B2 antibody Fab

Light chain of SN-131/1B2 antibody Fab