SMTL ID : 6fzr.1

Crystal structure of scFv-SM3 in complex with compound 2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

ALA-PRO-ASP-THR-ARG-PRO.1: 9 residues within 4Å: Chain A: N.31, Y.32, W.33, L.53, Q.103, Y.168, W.227, W.232 Ligands: EEQ.10 11 PLIP interactions: 11 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:N.31, A:W.33, A:Q.103, A:Y.168 Water bridges: A:G.102

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

EDO.2: 3 residues within 4Å: Chain A: S.7, G.8, G.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.8, A:G.9 EDO.3: 6 residues within 4Å: Chain A: L.45, E.46, W.47, W.232, V.233, F.234 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.47, A:F.234 Water bridges: A:F.234 EDO.4: 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.5: 3 residues within 4Å: Chain A: Q.109, G.110, T.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.110 Water bridges: A:T.112 EDO.6: 6 residues within 4Å: Chain A: T.139, Q.140, E.141, T.155, R.157, K.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.155, A:T.155, A:K.206 EDO.7: 2 residues within 4Å: Chain A: G.204, D.205 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.205 EDO.8: 3 residues within 4Å: Chain A: G.186, N.188, N.189 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.186, A:N.189 EDO.9: 3 residues within 4Å: Chain A: T.151, V.152, T.153 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.151, A:T.153 Water bridges: A:T.153

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

EEQ.10: 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 No protein-ligand interaction detected (PLIP)

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-SM3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

scFv-SM3

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