SMTL ID : 7brs.1 (3 other biounits)

E.coli beta-galactosidase (E537Q) in complex with fluorescent probe KSA02

Coordinates

PDB Format Compare

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)

F4X.1: 17 residues within 4Å: Chain A: N.104, V.105, D.203, H.420, E.463, M.504, Y.505, Q.539, H.542, W.570, F.603, N.606, V.797, D.804, W.1001 Ligands: NA.4, DMS.14 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:V.105, A:V.797, A:W.1001 Hydrogen bonds: A:N.104, A:D.203, A:Y.505, A:Y.505, A:Q.539, A:F.603, A:N.606 Water bridges: A:D.203, A:H.420, A:N.462 Salt bridges: A:H.420 pi-Stacking: A:W.1001

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.104, E.418, H.420, E.463 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.420, A:E.463, H2O.1, H2O.2, H2O.2 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

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

NA.4: 6 residues within 4Å: Chain A: Y.102, D.203, W.570, F.603, N.606 Ligands: F4X.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.102, A:W.570, A:N.606

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

DMS.5: 4 residues within 4Å: Chain A: S.55, L.56, N.57, G.58 No protein-ligand interaction detected (PLIP) DMS.6: 7 residues within 4Å: Chain A: P.34, F.35, A.36, W.38, D.47, E.328, A.329 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.47 DMS.7: 6 residues within 4Å: Chain A: R.559, H.624, Q.625, Q.627, Q.630, Q.720 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.559, A:R.559, A:Q.630 pi-Cation interactions: A:H.624 DMS.8: 8 residues within 4Å: Chain A: V.229, T.231, V.332, G.333, R.450, N.451, P.453, R.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.333 DMS.9: 3 residues within 4Å: Chain A: V.86, V.87, H.95 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.87 pi-Cation interactions: A:H.95 DMS.10: 1 residues within 4Å: Chain A: D.430 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.430 DMS.11: 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:E.279 DMS.12: 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.13: 5 residues within 4Å: Chain A: E.336, V.337, R.338, P.482, S.483 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.337 Salt bridges: A:E.336 DMS.14: 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.15: 4 residues within 4Å: Chain A: G.530, E.531, T.532, R.533 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.532, A:R.533 Salt bridges: A:E.531 DMS.16: 5 residues within 4Å: Chain A: Y.107, P.108, I.109, T.110, P.598 No protein-ligand interaction detected (PLIP) DMS.17: 4 residues within 4Å: Chain A: D.430, H.466, G.467, A.468 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.430 DMS.18: 1 residues within 4Å: Chain A: Q.14 No protein-ligand interaction detected (PLIP) DMS.19: 6 residues within 4Å: Chain A: R.232, F.233, N.234, R.239, A.240, V.241 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.241

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 2 residues within 4Å: Chain A: N.27, W.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.27

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
A

Beta-galactosidase

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