SMTL ID : 6kuz.1 (1 other biounit)

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSL01

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)

DVL.1: 18 residues within 4Å: Chain A: N.103, D.202, H.392, H.419, M.424, N.461, E.462, M.503, Y.504, Q.538, H.541, W.569, N.605, W.1000 Chain D: E.282, R.283 Ligands: NA.2, MG.18 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.103, A:D.202, A:H.392, A:N.461, A:E.462, A:Y.504, A:Q.538, A:Q.538, A:H.541 Water bridges: A:D.202 Salt bridges: A:H.419 pi-Stacking: A:W.1000 pi-Cation interactions: A:H.419 DVL.20: 18 residues within 4Å: Chain B: N.103, D.202, H.392, E.417, H.419, N.461, E.462, M.503, Y.504, Q.538, H.541, W.569, N.605, W.1000 Chain C: E.282, R.283 Ligands: NA.21, MG.32 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.103, B:D.202, B:E.417, B:N.461, B:Y.504, B:Q.538, B:Q.538, B:Q.538 pi-Stacking: B:W.1000 pi-Cation interactions: B:H.419 Hydrophobic interactions: C:E.282, C:R.283 DVL.34: 18 residues within 4Å: Chain B: E.282, R.283 Chain C: N.103, D.202, H.392, H.419, M.424, N.461, E.462, M.503, Y.504, Q.538, H.541, W.569, N.605, W.1000 Ligands: NA.35, MG.51 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.103, C:H.392, C:N.461, C:Q.538, C:Q.538, C:H.541 Water bridges: C:D.202, C:H.419, C:E.462 Salt bridges: C:H.419 pi-Stacking: C:W.1000 pi-Cation interactions: C:H.419 DVL.53: 18 residues within 4Å: Chain A: E.282, R.283 Chain D: N.103, D.202, H.392, E.417, H.419, N.461, E.462, M.503, Y.504, Q.538, H.541, W.569, N.605, W.1000 Ligands: NA.54, MG.65 16 PLIP interactions: 14 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.103, D:D.202, D:D.202, D:E.417, D:N.461, D:E.462, D:Y.504, D:Y.504, D:Q.538, D:Q.538, D:Q.538 Water bridges: D:H.419 pi-Stacking: D:W.1000 pi-Cation interactions: D:H.419 Hydrophobic interactions: A:E.282, A:R.283

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.605, 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:R.558 NA.4: 4 residues within 4Å: Chain A: S.648, E.651, L.671 Ligands: DMS.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.648, A:E.651, A:L.671 NA.21: 5 residues within 4Å: Chain B: Y.101, D.202, F.602, N.605 Ligands: DVL.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.602, B:N.605 NA.22: 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:F.557 NA.23: 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.35: 5 residues within 4Å: Chain C: Y.101, D.202, F.602, N.605 Ligands: DVL.34 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.202, C:N.605 NA.36: 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.37: 4 residues within 4Å: Chain C: S.648, E.651, L.671 Ligands: DMS.38 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.648, C:E.651, C:L.671 NA.54: 5 residues within 4Å: Chain D: Y.101, D.202, F.602, N.605 Ligands: DVL.53 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.101, D:N.605, D:N.605 NA.55: 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:P.561 NA.56: 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

42 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: S.648, D.649, N.650, E.651, L.652, P.704, N.705 Ligands: NA.4 Ligand excluded by PLIP DMS.6: 3 residues within 4Å: Chain A: A.35, D.46, R.47 Ligand excluded by PLIP DMS.7: 3 residues within 4Å: Chain A: T.258, H.317, G.321 Ligand excluded by PLIP DMS.8: 3 residues within 4Å: Chain A: Y.106, T.109, P.597 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: T.272, T.291, L.292, R.293 Ligand excluded by PLIP DMS.10: 4 residues within 4Å: Chain A: D.83, H.94, G.95, Y.96 Ligand excluded by PLIP DMS.11: 3 residues within 4Å: Chain A: V.336, R.337, P.481 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain A: I.306, P.307, N.308 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: R.426 Chain D: L.251, A.287, D.288 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: I.738, E.751, L.752, G.753 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: K.381, N.384, F.627, Y.643, W.709 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: R.38, Q.51, S.133, W.134, H.217 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: Q.825, R.854 Chain B: L.731, P.732 Ligand excluded by PLIP DMS.24: 8 residues within 4Å: Chain B: V.228, T.230, V.331, G.332, R.334, R.449, N.450, P.452 Ligand excluded by PLIP DMS.25: 3 residues within 4Å: Chain B: T.619, K.622, W.718 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain B: I.577, P.585, W.586, S.587, R.974 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain B: D.429 Chain C: H.227, R.449, V.479 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain B: L.378, A.708, W.709, S.710, E.711 Ligand excluded by PLIP DMS.29: 2 residues within 4Å: Chain B: R.426 Chain C: D.288 Ligand excluded by PLIP DMS.30: 2 residues within 4Å: Chain B: N.897, N.946 Ligand excluded by PLIP DMS.31: 3 residues within 4Å: Chain B: I.794, S.797, E.809 Ligand excluded by PLIP DMS.38: 8 residues within 4Å: Chain C: S.648, D.649, N.650, E.651, L.652, P.704, N.705 Ligands: NA.37 Ligand excluded by PLIP DMS.39: 3 residues within 4Å: Chain C: A.35, D.46, R.47 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain C: T.258, H.317, G.321 Ligand excluded by PLIP DMS.41: 3 residues within 4Å: Chain C: Y.106, T.109, P.597 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain C: T.272, T.291, L.292, R.293 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain C: D.83, H.94, G.95, Y.96 Ligand excluded by PLIP DMS.44: 3 residues within 4Å: Chain C: V.336, R.337, P.481 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain C: I.306, P.307, N.308 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain B: L.251, A.287, D.288 Chain C: R.426 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain C: I.738, E.751, L.752, G.753 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain C: K.381, N.384, F.627, Y.643, W.709 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain C: R.38, Q.51, S.133, W.134, H.217 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain C: Q.825, R.854 Chain D: L.731, P.732 Ligand excluded by PLIP DMS.57: 8 residues within 4Å: Chain D: V.228, T.230, V.331, G.332, R.334, R.449, N.450, P.452 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain D: T.619, K.622, W.718 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain D: I.577, P.585, W.586, S.587, R.974 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain A: H.227, R.449, V.479 Chain D: D.429 Ligand excluded by PLIP DMS.61: 5 residues within 4Å: Chain D: L.378, A.708, W.709, S.710, E.711 Ligand excluded by PLIP DMS.62: 2 residues within 4Å: Chain A: D.288 Chain D: R.426 Ligand excluded by PLIP DMS.63: 2 residues within 4Å: Chain D: N.897, N.946 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain D: I.794, S.797, E.809 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.18: 4 residues within 4Å: Chain A: E.417, H.419, E.462 Ligands: DVL.1 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.417, A:H.419, A:E.462, H2O.1, H2O.2, H2O.2 MG.19: 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.32: 6 residues within 4Å: Chain B: D.200, D.202, E.417, H.419, E.462 Ligands: DVL.20 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.417, B:H.419, B:E.462, H2O.6, H2O.7 MG.33: 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.51: 4 residues within 4Å: Chain C: E.417, H.419, E.462 Ligands: DVL.34 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.417, C:H.419, C:E.462, H2O.10, H2O.11, H2O.12 MG.52: 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.65: 6 residues within 4Å: Chain D: D.200, D.202, E.417, H.419, E.462 Ligands: DVL.53 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.417, D:H.419, D:E.462, H2O.16, H2O.17 MG.66: 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

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
A

B
B

C
A

D
B

Beta-galactosidase

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