SMTL ID : 6tr6.1

N-acetylserotonin-Notum complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: N.19, V.22 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

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

SO4.2: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.3: 3 residues within 4Å: Chain A: R.13, H.15, R.141 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.13, A:H.15, A:R.141 SO4.4: 2 residues within 4Å: Chain A: R.339, H.342 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.339, A:H.342 SO4.5: 4 residues within 4Å: Chain A: T.65, M.66, R.67, R.68 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.67, A:R.68 Water bridges: A:D.74 Salt bridges: A:R.68

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

EDO.6: 6 residues within 4Å: Chain A: W.260, I.315, R.317, W.320, V.323, L.330 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.317, A:R.317, A:W.320 Water bridges: A:D.187, A:E.313, A:V.323 EDO.7: 7 residues within 4Å: Chain A: R.79, T.80, G.81, T.82, L.85, F.102, I.316 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.79, A:R.79, A:T.82, A:T.82 Water bridges: A:T.80

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 4 residues within 4Å: Chain A: S.40, R.41, R.42, K.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.41, A:R.42, A:K.147 DMS.9: 6 residues within 4Å: Chain A: R.42, Y.94, W.95, W.96, N.97, A.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.97, A:A.98 pi-Cation interactions: A:W.96 DMS.10: 8 residues within 4Å: Chain A: Y.33, E.48, R.68, W.75, P.76, R.79, F.102, P.104 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.79 Salt bridges: A:E.48 pi-Cation interactions: A:W.75 DMS.11: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.198, A:R.198 Water bridges: A:Y.197

2 x ASE: N-ACETYL SEROTONIN(Non-covalent)

ASE.12: 6 residues within 4Å: Chain A: L.192, D.193, N.194, K.195, P.210, T.211 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.210, A:T.211 Hydrogen bonds: A:N.194, A:T.211 pi-Cation interactions: A:K.195 ASE.13: 11 residues within 4Å: Chain A: W.51, Y.52, V.110, A.156, T.159, F.191, P.210, F.242, F.243, A.265, V.269 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.51, A:Y.52, A:V.110, A:A.156, A:F.191, A:P.210, A:F.243, A:A.265, A:V.269 Hydrogen bonds: A:T.159 pi-Stacking: A:F.191, A:F.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural characterization of melatonin as an inhibitor of the Wnt deacylase Notum. J. Pineal Res. (2020)

Release Date

2020-01-08

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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