- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.67 Å
- Oligo State
- monomer
- Ligands
- 1 x F4X: 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 5 residues within 4Å:- Chain A: N.104, D.203, E.418, H.420, E.463
6 PLIP interactions:3 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: A:E.418, A:H.420, A:E.463, H2O.1, H2O.2, H2O.3
MG.3: 7 residues within 4Å:- Chain A: D.17, W.18, N.20, V.23, Y.163, Q.165, D.195
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.17, A:N.20, A:V.23, A:D.195
- 2 x NA: SODIUM ION(Non-functional Binders)
NA.4: 6 residues within 4Å:- Chain A: Y.102, D.203, F.603, C.604, N.606
- Ligands: F4X.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.102, A:N.606
- Water bridges: A:Q.575
NA.5: 4 residues within 4Å:- Chain A: F.558, Y.561, P.562, L.564
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:P.562
- 12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.6: 9 residues within 4Å:- Chain A: T.231, V.332, G.333, R.335, R.450, N.451, H.452, P.453, R.484
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:G.333
DMS.7: 6 residues within 4Å:- Chain A: R.559, H.624, Q.625, Q.627, Q.630, Q.720
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.627, A:Q.630
DMS.8: 3 residues within 4Å:- Chain A: T.273, L.293, R.294
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.294
DMS.9: 3 residues within 4Å:- Chain A: E.59, L.127, T.128
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.128
DMS.10: 5 residues within 4Å:- Chain A: P.34, F.35, W.38, D.47, A.329
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:D.47
DMS.11: 6 residues within 4Å:- Chain A: K.382, N.385, F.386, F.628, Y.644, W.710
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Y.644
DMS.12: 3 residues within 4Å:- Chain A: L.56, N.57, L.127
No protein-ligand interaction detected (PLIP)DMS.13: 5 residues within 4Å:- Chain A: Y.474, T.496, T.498, D.499, R.533
No protein-ligand interaction detected (PLIP)DMS.14: 2 residues within 4Å:- Chain A: Q.14, R.15
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.14
DMS.15: 5 residues within 4Å:- Chain A: N.104, D.600, F.603, V.797
- Ligands: F4X.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.104
- Salt bridges: A:D.600
- pi-Cation interactions: A:F.603
DMS.16: 2 residues within 4Å:- Chain A: N.27, W.160
No protein-ligand interaction detected (PLIP)DMS.17: 3 residues within 4Å:- Chain A: F.514, K.519
- Ligands: F4X.1
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gao, Y. et al., Two-Dimensional Design Strategy to Construct Smart Fluorescent Probes for the Precise Tracking of Senescence. Angew.Chem.Int.Ed.Engl. (2021)
- Release Date
- 2021-03-03
- Peptides
- Beta-galactosidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
C
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.67 Å
- Oligo State
- monomer
- Ligands
- 1 x F4X: 8-[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-indol-1-ium-1-yl]octanoic acid(Non-covalent)
- 2 x MG: MAGNESIUM ION(Non-covalent)
- 2 x NA: SODIUM ION(Non-functional Binders)
- 12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Gao, Y. et al., Two-Dimensional Design Strategy to Construct Smart Fluorescent Probes for the Precise Tracking of Senescence. Angew.Chem.Int.Ed.Engl. (2021)
- Release Date
- 2021-03-03
- Peptides
- Beta-galactosidase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
C