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

Co-crystal structure of alpha glucosidase with compound 9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 6 residues within 4Å: Chain A: R.111, R.113, P.115 Chain C: Y.216, G.217, W.219 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:R.111, A:R.111, C:G.217 PGE.9: 6 residues within 4Å: Chain C: D.71, H.72, N.73, R.351 Chain D: L.105 Ligands: EDO.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.73 PGE.13: 5 residues within 4Å: Chain C: R.137, G.148, S.149, D.150, E.152 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.137, C:D.150, C:D.150 PGE.14: 7 residues within 4Å: Chain C: V.526, S.527, Q.559, K.561, D.591, W.592, S.593 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.559, C:K.561 PGE.27: 3 residues within 4Å: Chain C: S.394, E.396, D.397 2 PLIP interactions: 2 interactions with chain C Water bridges: C:S.394, C:E.396

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

EDO.2: 5 residues within 4Å: Chain A: V.87, E.89, R.101, D.103, R.113 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain B: D.62, F.64 Chain C: M.196, R.255 Ligands: WAV.7 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain B: K.48, V.49, T.50, E.54, Y.56, P.71 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain C: D.352, F.355 Ligands: PGE.9 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain C: N.73, F.355, V.469, R.470, R.471 Chain D: S.107, R.108 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain C: Y.435, R.544 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: K.95, D.96 Chain C: D.27, R.30, Q.31 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: K.477, D.478, D.500, T.538, P.539, I.540 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain C: R.468, D.478, P.480, P.539, W.541 Chain D: D.71 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain C: S.186, P.188 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: I.395, D.397, Q.398, Q.419, Y.421 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain C: P.441, Q.442 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: Q.370, K.373, E.374, E.496 Ligand excluded by PLIP EDO.24: 3 residues within 4Å: Chain C: G.246, F.505, Q.508 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain C: F.363, T.366, I.462, P.464, G.495, E.496 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: E.311, R.315, G.414, A.415, T.449, L.450 Ligand excluded by PLIP

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

SO4.3: 3 residues within 4Å: Chain A: H.179, R.181, A.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.182 Salt bridges: A:H.179 SO4.28: 6 residues within 4Å: Chain C: Y.369, K.373, Y.507, Q.508, H.511, F.513 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.369 Water bridges: C:K.373, C:D.531, C:D.531 Salt bridges: C:K.373 SO4.31: 4 residues within 4Å: Chain D: C.114, D.115, C.117, T.132 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.115

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 3 residues within 4Å: Chain B: F.64 Chain C: F.202 Ligands: WAV.7 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.202 PG4.8: 6 residues within 4Å: Chain C: P.539, W.541, K.583, G.585 Chain D: D.70, D.71 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.583

1 x WAV: (1S,2S,3R,4S,5S)-1-(hydroxymethyl)-5-{[2-(2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethoxy)ethyl]amino}cyclohexane-1,2,3,4-tetrol(Non-covalent)

WAV.7: 18 residues within 4Å: Chain C: W.54, D.82, I.83, I.119, W.154, C.155, W.156, W.193, D.195, M.196, F.202, R.255, W.268, D.271, F.304, H.329 Ligands: PG4.4, EDO.5 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.156, C:F.202 Hydrogen bonds: C:W.156, C:R.255, C:D.271, C:H.329 Water bridges: C:G.270, C:R.327 pi-Stacking: C:W.156

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

PEG.16: 3 residues within 4Å: Chain C: Q.385, D.403, R.458 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.385, C:D.403 Water bridges: C:V.384 PEG.20: 4 residues within 4Å: Chain C: S.391, I.395, Y.421, T.443 1 PLIP interactions: 1 interactions with chain C Water bridges: C:T.443 PEG.29: 5 residues within 4Å: Chain C: A.110, S.111, R.113 Chain D: G.112, T.127 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.111 PEG.30: 5 residues within 4Å: Chain D: C.73, D.74, C.75, K.76, P.88 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Water bridges: D:C.73, C:R.544

2 x CA: CALCIUM ION(Non-covalent)

CA.32: 6 residues within 4Å: Chain D: Q.67, D.70, Y.72, D.74, D.80, E.81 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:Q.67, D:D.70, D:Y.72, D:D.74, D:D.80, D:E.81 CA.33: 6 residues within 4Å: Chain D: R.108, D.111, V.113, D.115, D.121, E.122 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:R.108, D:D.111, D:V.113, D:D.115, D:D.121, D: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

2021-10-06

Peptides

Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1: A
Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2: B
Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3: C
Glucosidase 2 subunit beta: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
A

D
B

Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1

Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2

Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3

Glucosidase 2 subunit beta

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