- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.83 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x DVL: 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
NA.2: 5 residues within 4Å:- Chain A: Y.101, D.202, F.602, N.605
- Ligands: DVL.1
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.101, A:F.602, A:N.605
NA.3: 4 residues within 4Å:- Chain A: F.557, Y.560, P.561, L.563
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:P.561
NA.4: 3 residues within 4Å:- Chain A: S.648, E.651, L.671
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.651, A:E.651, A:L.671
NA.13: 5 residues within 4Å:- Chain B: Y.101, D.202, F.602, N.605
- Ligands: DVL.12
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.101, B:N.605, B:N.605
NA.14: 4 residues within 4Å:- Chain B: F.557, Y.560, P.561, L.563
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:L.563
NA.15: 5 residues within 4Å:- Chain B: F.932, P.933, L.968, M.969, T.971
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:L.968
NA.29: 5 residues within 4Å:- Chain C: Y.101, D.202, F.602, N.605
- Ligands: DVL.28
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:N.605, C:N.605
NA.30: 4 residues within 4Å:- Chain C: F.557, Y.560, P.561, L.563
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:P.561
NA.31: 3 residues within 4Å:- Chain C: S.648, E.651, L.671
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:E.651, C:E.651, C:L.671
NA.40: 5 residues within 4Å:- Chain D: Y.101, D.202, F.602, N.605
- Ligands: DVL.39
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:D.202, D:N.605
NA.41: 4 residues within 4Å:- Chain D: F.557, Y.560, P.561, L.563
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:Y.560
NA.42: 5 residues within 4Å:- Chain D: F.932, P.933, L.968, M.969, T.971
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:M.969
- 28 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.5: 5 residues within 4Å:- Chain A: R.38, Q.51, S.133, E.137, H.217
Ligand excluded by PLIPDMS.6: 3 residues within 4Å:- Chain A: H.94, G.95, Y.96
Ligand excluded by PLIPDMS.7: 6 residues within 4Å:- Chain A: S.54, L.55, N.56, E.58, L.126, F.128
Ligand excluded by PLIPDMS.8: 4 residues within 4Å:- Chain A: T.707, A.708, S.710, E.711
Ligand excluded by PLIPDMS.9: 5 residues within 4Å:- Chain A: K.381, N.384, F.627, Y.643, W.709
Ligand excluded by PLIPDMS.16: 6 residues within 4Å:- Chain B: S.648, D.649, N.650, E.651, P.704, N.705
Ligand excluded by PLIPDMS.17: 4 residues within 4Å:- Chain B: R.53, L.55, N.56, L.126
Ligand excluded by PLIPDMS.18: 5 residues within 4Å:- Chain B: T.105, Y.106, P.107, I.108, T.109
Ligand excluded by PLIPDMS.19: 5 residues within 4Å:- Chain B: G.276, G.277, E.278, V.290, T.291
Ligand excluded by PLIPDMS.20: 2 residues within 4Å:- Chain B: P.307, N.308
Ligand excluded by PLIPDMS.21: 5 residues within 4Å:- Chain B: W.37, D.46, R.47, P.48, S.49
Ligand excluded by PLIPDMS.22: 5 residues within 4Å:- Chain B: K.381, N.384, F.627, Y.643, W.709
Ligand excluded by PLIPDMS.23: 5 residues within 4Å:- Chain B: G.271, T.272, T.291, L.292, R.293
Ligand excluded by PLIPDMS.24: 6 residues within 4Å:- Chain B: V.228, T.230, G.332, R.334, N.450, P.452
Ligand excluded by PLIPDMS.32: 5 residues within 4Å:- Chain C: R.38, Q.51, S.133, E.137, H.217
Ligand excluded by PLIPDMS.33: 3 residues within 4Å:- Chain C: H.94, G.95, Y.96
Ligand excluded by PLIPDMS.34: 6 residues within 4Å:- Chain C: S.54, L.55, N.56, E.58, L.126, F.128
Ligand excluded by PLIPDMS.35: 4 residues within 4Å:- Chain C: T.707, A.708, S.710, E.711
Ligand excluded by PLIPDMS.36: 5 residues within 4Å:- Chain C: K.381, N.384, F.627, Y.643, W.709
Ligand excluded by PLIPDMS.43: 6 residues within 4Å:- Chain D: S.648, D.649, N.650, E.651, P.704, N.705
Ligand excluded by PLIPDMS.44: 4 residues within 4Å:- Chain D: R.53, L.55, N.56, L.126
Ligand excluded by PLIPDMS.45: 5 residues within 4Å:- Chain D: T.105, Y.106, P.107, I.108, T.109
Ligand excluded by PLIPDMS.46: 5 residues within 4Å:- Chain D: G.276, G.277, E.278, V.290, T.291
Ligand excluded by PLIPDMS.47: 2 residues within 4Å:- Chain D: P.307, N.308
Ligand excluded by PLIPDMS.48: 5 residues within 4Å:- Chain D: W.37, D.46, R.47, P.48, S.49
Ligand excluded by PLIPDMS.49: 5 residues within 4Å:- Chain D: K.381, N.384, F.627, Y.643, W.709
Ligand excluded by PLIPDMS.50: 5 residues within 4Å:- Chain D: G.271, T.272, T.291, L.292, R.293
Ligand excluded by PLIPDMS.51: 6 residues within 4Å:- Chain D: V.228, T.230, G.332, R.334, N.450, P.452
Ligand excluded by PLIP- 8 x MG: MAGNESIUM ION(Non-covalent)
MG.10: 6 residues within 4Å:- Chain A: D.200, D.202, E.417, H.419, E.462
- Ligands: DVL.1
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.417, A:H.419, A:E.462, H2O.1, H2O.2
MG.11: 7 residues within 4Å:- Chain A: D.16, W.17, N.19, V.22, Y.162, Q.164, D.194
4 PLIP interactions:4 interactions with chain A- Metal complexes: A:D.16, A:N.19, A:V.22, A:D.194
MG.26: 4 residues within 4Å:- Chain B: E.417, H.419, E.462
- Ligands: DVL.12
6 PLIP interactions:3 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:E.417, B:H.419, B:E.462, H2O.4, H2O.5, H2O.6
MG.27: 7 residues within 4Å:- Chain B: D.16, W.17, N.19, V.22, Y.162, Q.164, D.194
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:D.16, B:N.19, B:V.22, B:D.194
MG.37: 6 residues within 4Å:- Chain C: D.200, D.202, E.417, H.419, E.462
- Ligands: DVL.28
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:E.417, C:H.419, C:E.462, H2O.9, H2O.10
MG.38: 7 residues within 4Å:- Chain C: D.16, W.17, N.19, V.22, Y.162, Q.164, D.194
4 PLIP interactions:4 interactions with chain C- Metal complexes: C:D.16, C:N.19, C:V.22, C:D.194
MG.53: 4 residues within 4Å:- Chain D: E.417, H.419, E.462
- Ligands: DVL.39
6 PLIP interactions:3 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:E.417, D:H.419, D:E.462, H2O.12, H2O.13, H2O.14
MG.54: 7 residues within 4Å:- Chain D: D.16, W.17, N.19, V.22, Y.162, Q.164, D.194
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:D.16, D:N.19, D:V.22, D:D.194
- 2 x GOL: GLYCEROL(Non-functional Binders)
GOL.25: 5 residues within 4Å:- Chain B: R.231, F.232, N.233, R.238, V.240
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:R.231, B:R.231
GOL.52: 5 residues within 4Å:- Chain D: R.231, F.232, N.233, R.238, V.240
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:R.231, D:R.231
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Li, X. et al., First-generation species-selective chemical probes for fluorescence imaging of human senescence-associated beta-galactosidase. Chem Sci (2020)
- Release Date
- 2020-07-08
- Peptides
- Beta-galactosidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
DC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.83 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x DVL: 3-(1,3-benzothiazol-2-yl)-2-[[4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]methoxy]-5-methyl-benzaldehyde(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
- 28 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 8 x MG: MAGNESIUM ION(Non-covalent)
- 2 x GOL: GLYCEROL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Li, X. et al., First-generation species-selective chemical probes for fluorescence imaging of human senescence-associated beta-galactosidase. Chem Sci (2020)
- Release Date
- 2020-07-08
- Peptides
- Beta-galactosidase: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
DC
CD
D