- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.09 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.3: 3 residues within 4Å:- Chain A: R.132, D.133
- Ligands: SO4.4
No protein-ligand interaction detected (PLIP)PEG.14: 6 residues within 4Å:- Chain C: R.137, K.144, G.148, S.149, D.150, E.152
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:G.148, C:D.150
PEG.18: 5 residues within 4Å:- Chain C: A.110, S.111, R.113
- Chain D: G.112, T.127
2 PLIP interactions:2 interactions with chain D- Water bridges: D:C.114, D:T.127
PEG.20: 4 residues within 4Å:- Chain C: W.541, K.583, G.585
- Chain D: D.70
3 PLIP interactions:2 interactions with chain C, 1 interactions with chain D- Hydrogen bonds: C:K.583, C:G.585, D:D.70
PEG.22: 3 residues within 4Å:- Chain C: W.154, F.202, N.203
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:N.203
PEG.23: 5 residues within 4Å:- Chain A: N.36
- Chain C: F.202, V.207
- Ligands: SO4.6, WAS.27
No protein-ligand interaction detected (PLIP)PEG.26: 4 residues within 4Å:- Chain C: S.391, I.395, Y.421
- Ligands: EDO.25
1 PLIP interactions:1 interactions with chain C- Water bridges: C:T.443
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.4: 1 residues within 4Å:- Ligands: PEG.3
No protein-ligand interaction detected (PLIP)SO4.6: 7 residues within 4Å:- Chain B: D.62, F.64
- Chain C: M.196, F.202, V.207
- Ligands: PEG.23, WAS.27
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:D.62
SO4.30: 3 residues within 4Å:- Chain C: R.57, R.98
- Ligands: SO4.31
1 PLIP interactions:1 interactions with chain C- Salt bridges: C:R.98
SO4.31: 2 residues within 4Å:- Chain C: R.57
- Ligands: SO4.30
6 PLIP interactions:6 interactions with chain C- Water bridges: C:N.55, C:N.55, C:R.57, C:R.57, C:R.57
- Salt bridges: C:R.57
SO4.32: 4 residues within 4Å:- Chain C: P.100, P.102, E.184, G.185
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:P.100, C:E.184, C:E.184
- Water bridges: C:L.103
SO4.38: 5 residues within 4Å:- Chain D: C.114, D.115, C.116, C.117, T.132
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:D.115, D:T.132
- Water bridges: D:C.117
- 5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.9: 7 residues within 4Å:- Chain C: Y.435, M.467, F.484, R.544
- Chain D: C.73, P.88
- Ligands: EDO.34
1 PLIP interactions:1 interactions with chain C- Water bridges: C:R.544
PGE.12: 14 residues within 4Å:- Chain C: F.69, D.70, N.73, M.74, P.75, R.114, F.355, V.469, R.470, R.471
- Chain D: P.88, S.107, R.108
- Ligands: PGE.35
7 PLIP interactions:3 interactions with chain D, 4 interactions with chain C- Hydrogen bonds: D:P.88, D:S.107, D:R.108, C:F.69, C:N.73, C:M.74, C:R.114
PGE.17: 5 residues within 4Å:- Chain A: R.111, Y.112, R.113
- Chain C: Y.216, W.219
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.113
PGE.29: 3 residues within 4Å:- Chain C: S.394, E.396, D.397
No protein-ligand interaction detected (PLIP)PGE.35: 9 residues within 4Å:- Chain C: N.73
- Chain D: P.88, N.89, G.90, S.91, Y.103, L.105
- Ligands: PGE.12, PG4.13
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:P.88, D:Y.103
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x WAS: 2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethyl (2-{[(1S,2S,3R,4S,5S)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexyl]amino}ethyl)carbamate(Non-covalent)
WAS.27: 21 residues within 4Å:- Chain B: F.64
- Chain C: W.54, D.82, I.83, I.119, W.154, C.155, W.156, G.158, W.193, D.195, M.196, F.202, R.255, W.268, D.271, F.304, H.329, H.331
- Ligands: SO4.6, PEG.23
12 PLIP interactions:12 interactions with chain C- Hydrophobic interactions: C:W.156, C:F.202
- Hydrogen bonds: C:W.154, C:C.155, C:G.158, C:D.195, C:R.255, C:D.271, C:H.329
- Water bridges: C:G.270, C:D.271
- pi-Stacking: C:W.156
- 2 x CA: CALCIUM ION(Non-covalent)
CA.36: 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.37: 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
- 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
GB
HC
AD
B
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.09 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x WAS: 2-{[2-nitro-4-(triazan-1-yl)phenyl]amino}ethyl (2-{[(1S,2S,3R,4S,5S)-2,3,4,5-tetrahydroxy-5-(hydroxymethyl)cyclohexyl]amino}ethyl)carbamate(Non-covalent)
- 2 x CA: CALCIUM ION(Non-covalent)
- 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
GB
HC
AD
B