SMTL ID : 8etl.1 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x VND: (1S,2S,3R,4S,5S)-5-(butylamino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Non-covalent)

VND.1: 11 residues within 4Å: Chain A: P.414, F.423, W.425, D.426, G.586, D.588, W.728, W.733, E.785, F.800, W.803 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.425, A:W.425, A:G.586, A:D.588

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: G.171, E.172, N.173, S.174, S.197, E.198, A.199 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.173, A:E.198, A:A.199 GOL.3: 5 residues within 4Å: Chain A: R.544, F.547, D.548, D.628, Y.632 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: G.136, G.137, G.311 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.137, A:G.311 SO4.5: 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:E.182, A:N.183, A:E.188, A:G.189 SO4.6: 1 residues within 4Å: Chain A: W.259 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.259, A:N.263 SO4.7: 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 SO4.8: 6 residues within 4Å: Chain A: Y.407, L.452, W.458, I.459, A.460, Q.463 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.458, A:A.460 Water bridges: A:Y.407 SO4.9: 5 residues within 4Å: Chain A: N.496, Y.738, K.809, H.814, H.815 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.496 Salt bridges: A:K.809, A:H.815 SO4.10: 3 residues within 4Å: Chain A: R.225, W.259, A.280 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.225, A:R.225 Salt bridges: A:R.225 SO4.11: 4 residues within 4Å: Chain A: K.341, Y.745, T.749, R.759 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.745 Salt bridges: A:K.341, A:R.759

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
A

Chaetomium alpha glucosidase

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