SMTL ID : 3t2q.1

E. coli (lacZ) beta-galactosidase (S796D) in complex with galactonolactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x 149: D-galactonolactone(Non-covalent)

149.1: 13 residues within 4Å: Chain A: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.420, A:N.489, A:E.490 Water bridges: A:D.230, A:D.230, A:D.230 149.20: 13 residues within 4Å: Chain B: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.23 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.230, B:H.420, B:N.489, B:E.490 Water bridges: B:N.131, B:D.230, B:D.230 149.41: 14 residues within 4Å: Chain C: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.44 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.230, C:H.420, C:N.489, C:E.490 Water bridges: C:N.131, C:D.230, C:D.230, C:D.230 149.59: 14 residues within 4Å: Chain D: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: MG.60, NA.62 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.230, D:H.420, D:N.489, D:E.490 Water bridges: D:D.230, D:D.230

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.445, A:H.447, A:E.490, H2O.4, H2O.21, H2O.22 MG.3: 7 residues within 4Å: Chain A: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.44, A:N.47, A:V.50, A:D.222 MG.21: 4 residues within 4Å: Chain B: N.131, E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.445, B:H.447, B:E.490, H2O.25, H2O.27, H2O.42 MG.22: 7 residues within 4Å: Chain B: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.44, B:N.47, B:V.50, B:D.222 MG.42: 4 residues within 4Å: Chain C: N.131, E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.447, C:E.490, H2O.46, H2O.49, H2O.64 MG.43: 5 residues within 4Å: Chain C: D.44, N.47, V.50, Q.192, D.222 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.44, C:N.47, C:V.50, C:D.222 MG.60: 4 residues within 4Å: Chain D: E.445, H.447, E.490 Ligands: 149.59 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.445, D:H.447, D:E.490, H2O.67, H2O.83, H2O.83 MG.61: 6 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, Q.192, D.222 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.44, D:N.47, D:V.50, D:D.222

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

NA.4: 6 residues within 4Å: Chain A: Y.129, D.230, W.597, F.630, N.633 Ligands: 149.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.630, A:N.633 NA.5: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.591, A:L.591 NA.6: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.999 NA.23: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: 149.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.630, B:N.633 NA.24: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.585 NA.25: 5 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.676, B:E.679 NA.44: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: 149.41 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.129, C:D.230, C:N.633 NA.45: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.591, C:L.591 NA.46: 5 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, L.699 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.679, C:E.679, C:L.699 NA.62: 6 residues within 4Å: Chain D: Y.129, D.230, W.597, F.630, N.633 Ligands: 149.59 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.230, D:N.633 NA.63: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.589 Water bridges: D:Q.592

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

DMS.7: 8 residues within 4Å: Chain A: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.10: 7 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.15 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: G.299, T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: R.81, S.82, L.83, N.84, L.154 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.15: 7 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.10 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: E.86, W.87, L.154, T.155 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: R.311, G.312, G.313, A.315 Chain D: V.450 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain A: R.433, Y.434 Ligand excluded by PLIP DMS.26: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.657 Ligand excluded by PLIP DMS.28: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.29: 8 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.39 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain B: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain B: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain B: L.83, N.84, E.86, L.154, F.156 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain B: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain B: G.304, V.318, T.319, R.321 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: Q.474, R.477, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: R.477, W.503, V.507 Ligand excluded by PLIP DMS.38: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.39: 6 residues within 4Å: Chain B: A.63, D.74, R.75, P.76, S.77 Ligands: DMS.29 Ligand excluded by PLIP DMS.40: 2 residues within 4Å: Chain B: P.335, N.336 Ligand excluded by PLIP DMS.47: 9 residues within 4Å: Chain C: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain C: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.50: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.57 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.53: 7 residues within 4Å: Chain C: R.81, S.82, L.83, N.84, L.154, T.155, F.156 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain C: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain C: G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain C: D.74, R.75, P.76, S.77 Ligands: DMS.50 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain C: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.64: 9 residues within 4Å: Chain D: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.66: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.67: 8 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.72 Ligand excluded by PLIP DMS.68: 4 residues within 4Å: Chain D: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain D: S.82, L.83, N.84, W.87, L.154 Ligand excluded by PLIP DMS.70: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain D: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.72: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.67 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jancewicz, L.J. et al., Ser-796 of Beta-Galactosidase (E. coli) Plays a Key Role in Maintaining an Optimum Balance between the Opened and Closed Conformations of the Catalytically Important Active Site Loop. Arch.Biochem.Biophys. (2012)

Release Date

2012-01-18

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Beta-galactosidase

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