SMTL ID : 7btk.2 (3 other biounits)

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

monomer

Ligands

1 x F6L: 4-[[2-[(E)-2-[4-[(2S,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethenyl]-3,3-dimethyl-2H-indol-1-yl]methyl]benzoic acid(Non-covalent)

F6L.1: 17 residues within 4Å: Chain A: N.104, D.203, H.393, E.418, N.462, E.463, Y.505, F.514, K.519, Q.539, H.542, W.570, N.606, N.806, W.1001 Ligands: MG.2, NA.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:F.514, A:F.514, A:W.1001 Hydrogen bonds: A:N.104, A:D.203, A:E.418, A:N.462, A:Y.505, A:Y.505, A:Q.539, A:H.542, A:N.606, A:N.806 Water bridges: A:H.420 pi-Stacking: A:F.514, A:W.1001 pi-Cation interactions: A:H.420

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: D.203, E.418, H.420, E.463 Ligands: F6L.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.418, A:H.420, A:E.463, H2O.3, H2O.6

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: Y.102, D.203, F.603, N.606 Ligands: F6L.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.102, A:N.606, A:N.606

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

DMS.4: 4 residues within 4Å: Chain A: S.55, L.56, N.57, L.127 No protein-ligand interaction detected (PLIP) DMS.5: 7 residues within 4Å: Chain A: V.229, T.231, V.332, G.333, R.450, N.451, R.484 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.335, A:R.484 Water bridges: A:R.335 DMS.6: 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.7: 6 residues within 4Å: Chain A: G.277, G.278, E.279, V.291, T.292, R.294 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.292 Water bridges: A:R.294 DMS.8: 5 residues within 4Å: Chain A: K.382, N.385, F.628, Y.644, W.710 No protein-ligand interaction detected (PLIP) DMS.9: 4 residues within 4Å: Chain A: T.85, V.86, V.87, H.95 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:H.95 DMS.10: 4 residues within 4Å: Chain A: D.47, R.48, P.49, S.50 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.47 DMS.11: 3 residues within 4Å: Chain A: H.95, G.96, Y.97 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:Y.97 DMS.12: 4 residues within 4Å: Chain A: Q.93, M.94, I.578, F.594 No protein-ligand interaction detected (PLIP) DMS.13: 2 residues within 4Å: Chain A: R.450, V.480 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.450 Water bridges: A:Q.247

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 6 residues within 4Å: Chain A: I.795, E.799, A.800, V.809, E.810, K.813 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.799, A:K.813

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
B

Beta-galactosidase

Related Entries With Identical Sequence