SMTL ID : 6y6s.1

Mouse Galactocerebrosidase complexed with galacto-noeurostegine GNS at pH 6.8

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: R.23, K.234, I.267, N.268, N.270 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 8 residues within 4Å: Chain A: T.527, N.528, K.606, G.607, Y.608, Y.627, A.653, R.654 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.608 NAG-NAG.3: 5 residues within 4Å: Chain A: D.345, L.347, G.348, N.349, L.439 No protein-ligand interaction detected (PLIP)

1 x ODW: (1~{R},2~{S},3~{S},4~{R},5~{R})-4-(hydroxymethyl)-8-azabicyclo[3.2.1]octane-1,2,3-triol(Non-covalent)

ODW.4: 14 residues within 4Å: Chain A: G.34, T.78, T.79, W.121, N.167, E.168, Y.224, E.244, S.247, W.277, Y.289, I.365, R.366, W.510 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.510 Hydrogen bonds: A:G.34, A:T.79, A:W.121, A:N.167, A:E.244, A:S.247, A:Y.289, A:R.366, A:R.366

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

NAG.5: 2 residues within 4Å: Chain A: Y.371, N.373 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.371 Hydrogen bonds: A:Y.371 Water bridges: A:N.373

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: D.463, N.465, F.497, D.646 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.463, A:F.497, A:D.646, H2O.5, H2O.6

1 x NI: NICKEL (II) ION(Non-covalent)

NI.7: 2 residues within 4Å: Chain A: H.524, H.630 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.524, A:H.630

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viuff, A. et al., The Bicyclic Form of galacto -Noeurostegine Is a Potent Inhibitor of beta-Galactocerebrosidase. Acs Med.Chem.Lett. (2021)

Release Date

2021-01-13

Peptides

Galactocerebrosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Galactocerebrosidase

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