SMTL ID : 8e3p.1 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x UF6: (2S,3S,4S,5R)-2-(hydroxymethyl)-1-{6-[3-nitro-5-(pyridin-4-yl)anilino]hexyl}piperidine-3,4,5-triol(Non-covalent)

UF6.1: 16 residues within 4Å: Chain A: P.414, F.418, F.419, F.423, W.425, D.426, K.472, G.586, D.588, Y.727, W.728, W.733, E.785, T.797, F.800, W.803 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.419, A:F.423, A:F.423, A:T.797 Hydrogen bonds: A:W.425, A:W.425, A:D.588 Water bridges: A:E.785 Salt bridges: A:D.426, A:D.588, A:E.785

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.146, T.208, K.209, G.210, F.301, D.302 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.146, A:T.208, A:G.210, A:D.302

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

SO4.3: 5 residues within 4Å: Chain A: G.369, H.370, G.466, A.467, R.470 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.370, A:A.467 Water bridges: A:Y.368, A:E.468 Salt bridges: A:H.370, A:R.470 SO4.4: 4 residues within 4Å: Chain A: T.578, V.579, S.580, H.581 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.578, A:T.578, A:V.579, A:S.580 Salt bridges: A:H.581 SO4.5: 6 residues within 4Å: Chain A: Y.407, L.452, W.458, I.459, A.460, Q.463 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.452, A:A.460, A:Q.463 Water bridges: A:Y.407 SO4.6: 7 residues within 4Å: Chain A: E.170, G.171, E.172, N.173, S.174, S.197, E.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.173, A:S.174, A:S.174, A:E.198 SO4.7: 3 residues within 4Å: Chain A: N.496, K.809, H.815 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.809, A:H.815

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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