SMTL ID : 7l9e.1

Crystal structure of apo-alpha glucosidase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: Y.112, R.113, P.115 Chain C: W.219 Ligand excluded by PLIP EDO.2: 4 residues within 4Å: Chain A: K.95 Chain C: D.27, R.30, Q.31 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: V.87, E.89, R.101, I.102, D.103, R.113 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain B: E.33, H.34, V.35, R.46, L.47, V.49 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain C: V.526, S.527, Q.559, D.591, W.592, S.593 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain C: Y.430, K.437, L.487, S.488, P.489, G.549 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain C: F.363, T.366, I.462, P.464, G.495, E.496 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain C: Y.369, Q.370, K.373, E.374, E.496, L.515 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain C: M.234, R.263, F.264 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain C: R.169, W.173 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain C: E.135, W.173, N.176, M.177, N.182 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain C: N.73, M.74, F.355, V.469, R.470, R.471 Chain D: S.107, R.108 Ligand excluded by PLIP EDO.17: 8 residues within 4Å: Chain C: W.54, D.82, I.83, I.119, W.193, D.195, F.304, H.329 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain D: E.122, Y.123, N.124, S.125, G.126, T.127, V.128 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain E: K.38 Chain F: E.7, T.8, F.9, H.12, S.13, D.14 Chain G: P.205 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain G: F.363, Q.370, I.462, P.464, E.496 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain G: F.180, P.188 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain G: R.131, W.173, N.176, M.177, N.182 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain G: K.115, P.188, N.189, Y.191, E.248, H.503 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain G: A.110, S.111 Chain H: G.112, T.127 Ligand excluded by PLIP EDO.29: 7 residues within 4Å: Chain G: N.73, F.355, V.469, R.470, R.471 Chain H: S.107, R.108 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain E: Y.112, P.115, D.116 Chain G: T.166, R.171, Y.231 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain G: W.54, D.82, I.83, I.119, W.156, W.193, D.195, F.304, H.329 Ligand excluded by PLIP

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

PEG.6: 4 residues within 4Å: Chain C: W.541, K.583, G.585 Chain D: D.70 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.583 PEG.8: 5 residues within 4Å: Chain C: A.110, S.111, R.113 Chain D: G.112, T.127 No protein-ligand interaction detected (PLIP) PEG.9: 6 residues within 4Å: Chain C: Y.369, K.373, Y.507, F.513, D.531, K.533 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.373, C:K.533

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

PG4.13: 3 residues within 4Å: Chain C: W.154, F.202, N.203 No protein-ligand interaction detected (PLIP)

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

SO4.18: 3 residues within 4Å: Chain C: R.98 Chain G: R.98 Ligands: SO4.19 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain C Salt bridges: G:R.98, C:R.98 SO4.19: 3 residues within 4Å: Chain C: R.57 Chain G: R.57 Ligands: SO4.18 2 PLIP interactions: 2 interactions with chain G Water bridges: G:N.55 Salt bridges: G:R.57 SO4.32: 8 residues within 4Å: Chain G: L.44, Y.365, W.466, K.477, L.499, D.500, G.502, I.540 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.500, G:D.500

4 x CA: CALCIUM ION(Non-covalent)

CA.20: 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.21: 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 CA.33: 6 residues within 4Å: Chain H: Q.67, D.70, Y.72, D.74, D.80, E.81 6 PLIP interactions: 6 interactions with chain H Metal complexes: H:Q.67, H:D.70, H:Y.72, H:D.74, H:D.80, H:E.81 CA.34: 6 residues within 4Å: Chain H: R.108, D.111, V.113, D.115, D.121, E.122 6 PLIP interactions: 6 interactions with chain H Metal complexes: H:R.108, H:D.111, H:V.113, H:D.115, H:D.121, H: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

2021-12-29

Peptides

Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #1: AE
Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #2: BF
Neutral alpha-glucosidase AB Trypsin-cleaved Fragment #3: CG
Glucosidase 2 subunit beta: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

E
G

B
F

F
H

C
A

G
C

D
B

H
D

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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