SMTL ID : 7kry.1 (1 other biounit)

Co-crystal structure of alpha glucosidase with compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

hetero-1-1-mer

Ligands

1 x X8Y: (1S,2S,3R,4S,5S)-5-({6-[(4-azido-2-nitrophenyl)amino]hexyl}amino)-1-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol(Non-covalent)

X8Y.1: 19 residues within 4Å: Chain A: F.284, W.400, D.428, I.429, I.465, W.500, C.501, W.502, W.539, D.541, M.542, F.548, R.601, W.614, D.617, F.650, F.651, H.675 Ligands: EDO.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.284, A:W.502, A:W.502, A:F.548, A:F.650, A:F.651 Hydrogen bonds: A:D.428, A:W.500, A:D.541, A:D.541, A:R.601, A:H.675, A:H.675 pi-Stacking: A:W.502

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 3 residues within 4Å: Chain A: L.678, D.679 Ligands: X8Y.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.679 EDO.3: 2 residues within 4Å: Chain A: W.500, N.549 No protein-ligand interaction detected (PLIP) EDO.4: 5 residues within 4Å: Chain A: T.491, R.492, D.493, L.556, D.558 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.493 EDO.6: 3 residues within 4Å: Chain A: D.735, G.770, Q.771 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.771 Water bridges: A:G.770

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 2 residues within 4Å: Chain A: S.737, Y.767 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.737

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

SO4.7: 2 residues within 4Å: Chain A: R.444 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.444 SO4.8: 2 residues within 4Å: Chain A: R.403 Ligands: SO4.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.401, A:R.682, A:R.682 Salt bridges: A:R.403

2 x CA: CALCIUM ION(Non-covalent)

CA.9: 7 residues within 4Å: Chain A: R.928 Chain B: Q.67, D.70, Y.72, D.74, D.80, E.81 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:Q.67, B:D.70, B:Y.72, B:D.74, B:D.80, B:E.81 CA.10: 6 residues within 4Å: Chain B: R.108, D.111, V.113, D.115, D.121, E.122 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:R.108, B:D.111, B:V.113, B:D.115, B:D.121, B:E.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Karade, S.S. et al., N-Substituted Valiolamine Derivatives as Potent Inhibitors of Endoplasmic Reticulum alpha-Glucosidases I and II with Antiviral Activity. J.Med.Chem. (2021)

Release Date

2021-12-01

Peptides

Neutral alpha-glucosidase AB: A
Glucosidase 2 subunit beta: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Neutral alpha-glucosidase AB

Glucosidase 2 subunit beta

Related Entries With Identical Sequence