SMTL ID : 6tv4.1

CFF-Notum complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

monomer

Ligands

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

SO4.1: 7 residues within 4Å: Chain A: R.167, E.170, V.225, P.226, E.227, R.230 Ligands: GOL.18 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.227 Water bridges: A:R.167, A:R.167 Salt bridges: A:R.167, A:R.230 SO4.2: 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 SO4.3: 7 residues within 4Å: Chain A: R.56, K.120, N.121, E.122, Y.123, Y.220 Ligands: DMS.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.122, A:Y.220 Water bridges: A:R.56, A:Y.123 Salt bridges: A:R.56 SO4.4: 4 residues within 4Å: Chain A: R.13, L.34, K.35, E.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.36, A:E.36, A:E.36 Salt bridges: A:R.13 SO4.8: 5 residues within 4Å: Chain A: R.295, K.326, H.358, V.360, S.362 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:V.360 Water bridges: A:R.295, A:K.326, A:K.326, A:H.358 Salt bridges: A:R.295, A:K.326 SO4.9: 1 residues within 4Å: Chain A: K.120 No protein-ligand interaction detected (PLIP) SO4.10: 9 residues within 4Å: Chain A: R.42, P.93, Y.94, W.95, W.96, N.97, A.98 Ligands: GOL.17, GOL.21 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.42, A:P.93, A:W.96, A:N.97, A:A.98 SO4.11: 4 residues within 4Å: Chain A: P.351, P.356, V.357, H.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.357, A:H.358 Water bridges: A:L.352 SO4.12: 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 SO4.13: 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 SO4.14: 8 residues within 4Å: Chain A: Y.33, E.48, R.68, W.75, P.76, R.79, F.102, P.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.33, A:R.79 Water bridges: A:W.75, A:W.75 SO4.15: 5 residues within 4Å: Chain A: L.14, L.16, S.72, R.73, W.75 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.75, A:W.75

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

NAG.5: 7 residues within 4Å: Chain A: N.19, S.21, V.22, M.126, L.129, E.133, R.136 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.19

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

DMS.6: 6 residues within 4Å: Chain A: Y.248, L.251, R.252, S.253, P.254, V.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.255 Water bridges: A:Y.248 DMS.7: 3 residues within 4Å: Chain A: R.56, E.57 Ligands: SO4.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.56 Salt bridges: A:E.57

1 x CFF: CAFFEINE(Non-covalent)

CFF.16: 13 residues within 4Å: Chain A: W.51, Y.52, V.110, A.156, T.159, F.191, P.210, I.214, F.242, F.243, A.265, Q.266, V.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.159 pi-Stacking: A:F.191, A:F.191

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 7 residues within 4Å: Chain A: G.39, S.40, R.41, R.42, N.97, A.98 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41, A:R.42 GOL.18: 9 residues within 4Å: Chain A: D.166, E.170, P.226, E.227, R.228, T.250, L.251, R.252 Ligands: SO4.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.166, A:E.227, A:R.228, A:R.228 Water bridges: A:C.229 GOL.19: 3 residues within 4Å: Chain A: R.13, H.15, R.141 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.13, A:H.15 Water bridges: A:L.16 GOL.20: 1 residues within 4Å: Chain A: R.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.68, A:R.68 GOL.21: 8 residues within 4Å: Chain A: R.42, Y.94, W.95, H.335, D.338, R.339, H.342 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:H.335, A:H.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Caffeine inhibits Notum activity by binding at the catalytic pocket. Commun Biol (2020)

Release Date

2020-10-28

Peptides

Palmitoleoyl-protein carboxylesterase NOTUM: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Palmitoleoyl-protein carboxylesterase NOTUM

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