SMTL ID : 8eqx.2 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 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: 2 residues within 4Å: Chain A: N.47, R.66 No protein-ligand interaction detected (PLIP)

1 x WT5: (2R,3R,4R,5S)-2-(hydroxymethyl)-1-{[6-({[(5M)-3-methyl-5-(1H-pyrrol-2-yl)phenyl]amino}methyl)pyridin-2-yl]methyl}piperidine-3,4,5-triol(Non-covalent)

WT5.2: 15 residues within 4Å: Chain A: P.414, F.418, F.419, F.423, W.425, D.426, F.477, G.586, D.588, Y.727, W.728, E.785, T.797, F.800, W.803 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.418, A:F.423, A:F.477 Hydrogen bonds: A:W.425, A:D.426, A:T.797 Salt bridges: A:D.426, A:E.785 pi-Stacking: A:F.419

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: T.578, V.579, S.580, H.581 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.578, A:V.579, A:S.580 GOL.4: 4 residues within 4Å: Chain A: Y.237, V.241, P.247, Q.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.251 GOL.5: 2 residues within 4Å: Chain A: W.259, K.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.282, A:K.282

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

SO4.6: 8 residues within 4Å: Chain A: S.371, R.375, Y.407, L.452, W.458, I.459, A.460, Q.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.371, A:R.375, A:A.460, A:Q.463 SO4.7: 7 residues within 4Å: Chain A: S.181, E.182, N.183, G.186, Y.187, E.188, G.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.181, A:E.182, A:E.188, A:G.189 SO4.8: 5 residues within 4Å: Chain A: G.369, H.370, G.466, A.467, R.470 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.370, A:A.467 Salt bridges: A:H.370, A:R.470

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karade, S.S. et al., Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum alpha-Glucosidase I with Anti-SARS-CoV-2 Activity. J.Med.Chem. (2023)

Release Date

2023-02-22

Peptides

Chaetomium alpha glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Chaetomium alpha glucosidase

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