- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.09 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.4: 9 residues within 4Å:- Chain C: N.73, M.74, P.75, F.355, V.469, R.470, R.471
- Chain D: S.107, R.108
5 PLIP interactions:3 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:S.107, D:R.108, D:R.108, C:N.73
- Water bridges: C:D.70
PEG.7: 6 residues within 4Å:- Chain C: F.305, K.306, N.307, H.331, D.333, T.334
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:K.306, C:N.307
- Water bridges: C:N.307, C:G.335
PEG.13: 4 residues within 4Å:- Chain C: W.541, K.583, G.585
- Chain D: D.70
4 PLIP interactions:2 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:D.70, C:K.583
- Water bridges: D:D.71, C:P.539
PEG.14: 3 residues within 4Å:- Chain C: S.569, F.570, Q.571
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:F.570, C:Q.571
PEG.17: 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.18: 8 residues within 4Å:- Chain C: V.526, S.527, S.528, Q.559, K.561, D.591, W.592, S.593
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.561
- Water bridges: C:D.591
PEG.21: 3 residues within 4Å:- Chain C: W.154, F.202, N.203
No protein-ligand interaction detected (PLIP)- 2 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.23: 20 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: EDO.3
13 PLIP interactions:12 interactions with chain C, 1 interactions with chain B- Hydrophobic interactions: C:W.156, C:F.202
- Hydrogen bonds: C:W.154, C:W.154, C:W.154, C:G.158, C:R.255, C:D.271, C:H.329
- Water bridges: C:G.270, C:D.271, C:R.327, B:D.62
- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.24: 4 residues within 4Å:- Chain C: K.437, H.438, H.439, Q.442
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:K.437, C:H.439, C:Q.442
- Water bridges: C:H.438, C:H.438
- Salt bridges: C:K.437, C:H.438
SO4.25: 4 residues within 4Å:- Chain C: V.557, E.565, S.566, R.567
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:E.565
- Salt bridges: C:R.567
- 2 x CA: CALCIUM ION(Non-covalent)
CA.28: 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.29: 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
IB
JC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.09 Å
- Oligo State
- hetero-1-1-1-1-mer
- Ligands
- 15 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 7 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 2 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 SO4: SULFATE ION(Non-functional Binders)
- 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
IB
JC
CD
D