SMTL ID : 6fzq.1

Crystal structure of scFv-SM3 in complex with compound 3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- ASP- THR- ARG- PRO: Mucin-1(Non-covalent)

ALA-PRO-ASP-THR-ARG-PRO.1: 10 residues within 4Å: Chain A: N.31, Y.32, W.33, L.53, Q.103, Y.168, W.227, W.232 Ligands: EDO.4, EEN.12 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.32, A:W.33, A:Y.168, A:Y.168, A:Y.168, A:W.227, A:W.232 Hydrogen bonds: A:N.31, A:Y.32, A:W.33, A:Q.103, A:Y.168 Water bridges: A:W.33, A:G.102

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

EDO.2: 7 residues within 4Å: Chain A: K.43, L.45, E.46, W.47, W.232, V.233, F.234 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.43, A:W.47, A:W.232, A:F.234, A:F.234 EDO.3: 4 residues within 4Å: Chain A: I.51, Y.58, S.73, R.74 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.74 EDO.4: 7 residues within 4Å: Chain A: G.102, Q.103, G.186, N.189 Ligands: ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.103 EDO.5: 3 residues within 4Å: Chain A: G.186, N.188, N.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.188, A:N.189, A:N.189 EDO.6: 3 residues within 4Å: Chain A: V.137, V.138, T.139 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.138, A:G.236 EDO.7: 1 residues within 4Å: Chain A: T.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.153 EDO.8: 3 residues within 4Å: Chain A: T.146, S.147, E.150 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.147 Water bridges: A:T.145, A:T.146, A:T.146 EDO.9: 7 residues within 4Å: Chain A: T.139, Q.140, E.141, T.155, C.156, R.157, K.206 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.155, A:R.157, A:R.157, A:K.206 EDO.10: 3 residues within 4Å: Chain A: T.151, T.153, T.210 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.153, A:T.153 EDO.11: 1 residues within 4Å: Chain A: Q.215 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.215

1 x EEN: 2-deoxy-2-[(difluoroacetyl)amino]-alpha-D-galactopyranose(Non-covalent)

EEN.12: 4 residues within 4Å: Chain A: Y.168 Ligands: ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1, ALA-PRO-ASP-THR-ARG-PRO.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.168

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bermejo, I.A. et al., Water Sculpts the Distinctive Shapes and Dynamics of the Tumor-Associated Carbohydrate Tn Antigens: Implications for Their Molecular Recognition. J.Am.Chem.Soc. (2018)

Release Date

2019-02-20

Peptides

scFv-1SM3,scFv-1SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

scFv-1SM3,scFv-1SM3

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