SMTL ID : 8e3j.2 (1 other biounit)

Co-crystal structure of Chaetomium glucosidase with compound 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

monomer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: N.47, R.66, E.408 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 3 residues within 4Å: Chain A: Y.92, T.93, K.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.92, A:T.93, A:T.93 GOL.3: 2 residues within 4Å: Chain A: Y.237, Q.251 No protein-ligand interaction detected (PLIP) GOL.4: 2 residues within 4Å: Chain A: K.312, E.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.313 GOL.5: 3 residues within 4Å: Chain A: S.567, T.568, K.634 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.566, A:T.568

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

UGO.6: 16 residues within 4Å: Chain A: P.414, F.419, R.421, F.423, W.425, D.426, V.473, P.474, F.477, G.586, D.588, Y.727, W.728, E.785, F.800, W.803 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.419 Hydrogen bonds: A:W.425, A:D.426, A:G.586, A:Y.727, A:W.728 Salt bridges: A:D.426, A:D.588, A:E.785

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

SO4.7: 5 residues within 4Å: Chain A: G.369, H.370, G.466, A.467, R.470 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.370, A:G.466, A:A.467 Salt bridges: A:H.370, A:R.470 SO4.8: 3 residues within 4Å: Chain A: W.706, R.764, N.768 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.768 Salt bridges: A:R.764 SO4.9: 7 residues within 4Å: Chain A: S.371, 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:A.460, A:Q.463, A:Q.463 SO4.10: 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:S.580 Salt bridges: A:H.581 SO4.11: 7 residues within 4Å: Chain A: S.181, E.182, N.183, G.186, Y.187, E.188, G.189 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.182, A:E.188, A:G.189

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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