SMTL ID : 3t0b.1

E. coli (LacZ) beta-galactosidase (S796T) IPTG complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.447, A:E.490, H2O.1, H2O.3, H2O.32 MG.2: 6 residues within 4Å: Chain A: D.44, 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.23: 3 residues within 4Å: Chain B: 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.34, H2O.40, H2O.68 MG.24: 7 residues within 4Å: Chain B: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.44, B:N.47, B:V.50, B:D.222, B:D.222 MG.48: 3 residues within 4Å: Chain C: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.445, C:H.447, C:E.490, H2O.73, H2O.106, H2O.109 MG.49: 6 residues within 4Å: Chain C: D.44, N.47, V.50, Y.190, Q.192, D.222 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.44, C:N.47, C:V.50, C:D.222, C:D.222 MG.74: 3 residues within 4Å: Chain D: E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.447, D:E.490, H2O.112, H2O.115, H2O.143 MG.75: 7 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, Y.190, 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

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

NA.3: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: IPT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.129, A:N.633 NA.4: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.589 NA.5: 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:P.961 NA.25: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: IPT.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230, B:N.633 NA.26: 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.27: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.999 NA.28: 4 residues within 4Å: Chain B: S.676, D.677, E.679, L.699 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.676, B:E.679, B:L.699 NA.50: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: IPT.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.129, C:D.230, C:N.633 NA.51: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.589 NA.52: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.996, C:T.999 NA.53: 5 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, L.699 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.679, C:E.679 NA.76: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: IPT.79 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.129, D:N.633, D:N.633 NA.77: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.588 NA.78: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.999

4 x IPT: 1-methylethyl 1-thio-beta-D-galactopyranoside(Non-covalent)

IPT.6: 13 residues within 4Å: Chain A: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.1028 Hydrogen bonds: A:N.131, A:E.490, A:F.630, A:N.633 Water bridges: A:H.447, A:E.490, A:E.490 IPT.29: 12 residues within 4Å: Chain B: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, F.630, N.633, W.1028 Ligands: NA.25 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:W.1028 Hydrogen bonds: B:N.131, B:D.230, B:E.490, B:F.630, B:N.633 IPT.54: 13 residues within 4Å: Chain C: N.131, D.230, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.50, DMS.69 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:W.1028 Hydrogen bonds: C:N.131, C:E.490, C:Y.532, C:F.630, C:N.633 Water bridges: C:N.489, C:E.490 IPT.79: 12 residues within 4Å: Chain D: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, F.630, N.633, W.1028 Ligands: NA.76 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.1028 Hydrogen bonds: D:N.131, D:D.230, D:E.490, D:Y.532, D:F.630, D:N.633 Water bridges: D:H.447, D:E.490

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

DMS.7: 9 residues within 4Å: Chain A: V.256, T.258, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: K.409, N.412, 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.18 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.12: 6 residues within 4Å: Chain A: R.534, E.537, P.1030, S.1031, V.1032, Q.1037 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: D.457, P.459 Chain D: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.17: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.18: 8 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77, L.80 Ligands: DMS.10 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: D.811, Q.812, F.813, T.814, H.844 Ligand excluded by PLIP DMS.20: 2 residues within 4Å: Chain A: T.137, P.625 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: L.406, Q.410, T.735, A.736, W.737, S.738 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.30: 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.31: 5 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.32: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.33: 8 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.41 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain B: G.299, T.300, R.321, L.322 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain B: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.36: 4 residues within 4Å: Chain B: P.135, I.136, W.220 Ligands: DMS.44 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: G.304, V.318, T.319, R.321 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain B: A.63, W.65, D.74, R.75 Ligands: DMS.33 Ligand excluded by PLIP DMS.42: 6 residues within 4Å: Chain B: L.406, Q.410, T.735, A.736, W.737, S.738 Ligand excluded by PLIP DMS.43: 3 residues within 4Å: Chain B: V.113, V.114, H.122 Ligand excluded by PLIP DMS.44: 3 residues within 4Å: Chain B: Y.134, P.625 Ligands: DMS.36 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: R.259, F.260, N.261, R.266, V.268 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.56: 6 residues within 4Å: Chain C: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.57: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.68 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain C: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain C: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain C: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain C: P.135, I.136, W.220 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain C: G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain C: K.650, R.728, I.743, W.746 Ligand excluded by PLIP DMS.66: 5 residues within 4Å: Chain B: Q.474, W.503, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.67: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.68: 3 residues within 4Å: Chain C: D.74, P.76 Ligands: DMS.57 Ligand excluded by PLIP DMS.69: 3 residues within 4Å: Chain C: N.131, V.824 Ligands: IPT.54 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain C: E.86, W.87, R.88, T.112, L.154, T.155 Ligand excluded by PLIP DMS.71: 2 residues within 4Å: Chain C: R.280, D.281 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: Y.501, T.522, T.523, T.525, R.560 Ligand excluded by PLIP DMS.73: 5 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.80: 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.81: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.82: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.83: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.91 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain D: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.85: 4 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.87: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain D: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.89: 3 residues within 4Å: Chain D: V.113, V.114, H.122 Ligand excluded by PLIP DMS.90: 4 residues within 4Å: Chain D: K.650, R.728, I.743, W.746 Ligand excluded by PLIP DMS.91: 6 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76 Ligands: DMS.83 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.93: 6 residues within 4Å: Chain D: A.765, I.766, H.768, E.779, L.780, G.781 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.95: 6 residues within 4Å: Chain D: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jancewicz, L.J. et al., er-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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