SMTL ID : 7bap.1

Notum Fragment 648

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

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

SO4.1: 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 SO4.8: 5 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.220 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.122 Water bridges: A:R.56, A:Y.123, A:Y.123 Salt bridges: A:R.56 SO4.9: 4 residues within 4Å: Chain A: V.279, Q.280, E.281, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.281 Salt bridges: A:R.284 SO4.10: 3 residues within 4Å: Chain A: Y.197, R.198, L.283 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.197 Salt bridges: A:R.198

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

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

2 x S4V: ~{N}2-pyridin-2-ylbenzene-1,2-diamine(Covalent)(Non-covalent)

S4V.3: 8 residues within 4Å: Chain A: W.51, Y.52, N.58, S.61, R.62, D.204, I.206, T.207 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.51, A:D.204, A:I.206, A:T.207 Hydrogen bonds: A:N.58, A:N.58, A:D.204 S4V.4: 11 residues within 4Å: Chain A: W.51, Y.52, F.191, L.192, P.210, I.214, F.242, F.243, Q.266, V.269 Ligands: DMS.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.52, A:F.191, A:F.191, A:P.210, A:I.214, A:F.242, A:F.243, A:V.269, A:V.269 Hydrogen bonds: A:Y.52, A:Y.52

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

DMS.5: 5 residues within 4Å: Chain A: W.51, A.156, T.159, F.191 Ligands: S4V.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.51, A:A.156 DMS.6: 4 residues within 4Å: Chain A: P.351, P.356, V.357, H.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.357, A:H.358 DMS.7: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Structural Analysis and Development of Notum Fragment Screening Hits. Acs Chem Neurosci (2022)

Release Date

2022-01-12

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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