SMTL ID : 6tr5.1

Melatonin-Notum complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

2 x ML1: N-[2-(5-methoxy-1H-indol-3-yl)ethyl]acetamide(Non-covalent)

ML1.1: 6 residues within 4Å: Chain A: L.192, D.193, N.194, K.195, P.210, T.211 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.194, A:T.211 ML1.2: 11 residues within 4Å: Chain A: W.51, Y.52, V.110, S.155, A.156, T.159, F.191, P.210, F.242, A.265, V.269 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.52, A:V.110, A:A.156, A:F.191, A:F.191, A:F.191, A:P.210, A:V.269 Hydrogen bonds: A:F.242 Water bridges: A:A.156

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

DMS.3: 6 residues within 4Å: Chain A: Y.33, R.68, W.75, P.76, R.79, P.104 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.48 pi-Cation interactions: A:W.75

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

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

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

SO4.5: 3 residues within 4Å: Chain A: R.295, K.326, V.360 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.360 Water bridges: A:K.326, A:V.360 Salt bridges: A:R.295, A:K.326 SO4.6: 3 residues within 4Å: Chain A: V.279, Q.280, E.281 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.281 SO4.7: 4 residues within 4Å: Chain A: R.167, E.170, V.225, E.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.227 Salt bridges: A:R.167 SO4.8: 3 residues within 4Å: Chain A: R.317, S.318, H.319 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.318, A:H.319 Salt bridges: A:H.319 SO4.9: 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 SO4.10: 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 SO4.11: 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 SO4.12: 5 residues within 4Å: Chain A: R.13, L.34, K.35, E.36, R.38 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36 Salt bridges: A:R.13, A:R.38

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

2020-01-15

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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