SMTL ID : 3t08.1

E. coli (LacZ) beta-galactosidase (S796A) IPTG complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.24, H2O.25, H2O.27 MG.2: 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.27: 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.35, H2O.51, H2O.57 MG.28: 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.29: 1 residues within 4Å: Chain B: E.398 No protein-ligand interaction detected (PLIP) MG.53: 4 residues within 4Å: Chain C: N.131, 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.88, H2O.89, H2O.90 MG.54: 7 residues within 4Å: Chain C: D.44, W.45, 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.79: 3 residues within 4Å: Chain D: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.445, D:H.447, D:E.490, H2O.93, H2O.112, H2O.117 MG.80: 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

13 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.591, A:L.591 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:T.999 NA.30: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: IPT.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230, B:N.633 NA.31: 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:P.589 NA.32: 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:P.961 NA.55: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: IPT.59 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.129, C:W.597, C:N.633 NA.56: 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:F.585 NA.57: 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:P.961, C:T.999 NA.58: 5 residues within 4Å: Chain C: S.676, D.677, E.679, L.699 Ligands: DMS.73 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.679, C:L.699, C:L.699 NA.81: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: IPT.84 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.129, D:W.597, D:N.633 NA.82: 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:Y.588, D:L.591 NA.83: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:M.997, 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 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.1028 Hydrogen bonds: A:N.131, A:D.230, A:E.490, A:F.630, A:N.633 Water bridges: A:H.447, A:N.489, A:E.490, A:E.490 IPT.33: 13 residues within 4Å: Chain B: 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.30 11 PLIP interactions: 11 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 Water bridges: B:D.230, B:H.420, B:H.447, B:E.490, B:E.490 IPT.59: 12 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.55 9 PLIP interactions: 9 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:H.447, C:E.490, C:E.490 IPT.84: 13 residues within 4Å: Chain D: 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.81 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:W.1028 Hydrogen bonds: D:N.131, D:E.490, D:Y.532, D:F.630, D:N.633 Water bridges: D:D.230, D:H.420, D:N.489, D:E.490, D:E.490, D:E.490

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

DMS.7: 10 residues within 4Å: Chain A: T.258, D.358, V.359, G.360, R.362, R.477, N.478, H.479, 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: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.20 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.16: 6 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: Y.134, I.136, T.137, P.625 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: K.650, I.743, W.746 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.20: 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.21: 4 residues within 4Å: Chain A: E.86, R.88, L.154, T.155 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain A: G.375, P.377 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.26: 3 residues within 4Å: Chain A: R.311, G.313 Chain D: V.450 Ligand excluded by PLIP DMS.34: 8 residues within 4Å: Chain B: V.256, T.258, V.359, G.360, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.35: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.37: 7 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.48 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.39: 2 residues within 4Å: Chain B: H.345, G.349 Ligand excluded by PLIP DMS.40: 6 residues within 4Å: Chain B: S.82, L.83, N.84, E.86, L.154, F.156 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain B: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.42: 3 residues within 4Å: Chain B: P.135, P.144 Ligands: DMS.45 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain B: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.44: 6 residues within 4Å: Chain B: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain B: G.622, D.623, T.624 Ligands: DMS.42 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: D.677, N.678, E.679, N.733 Ligand excluded by PLIP DMS.48: 7 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.37 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.51: 2 residues within 4Å: Chain B: P.957, R.1002 Ligand excluded by PLIP DMS.52: 7 residues within 4Å: Chain B: D.457, P.459 Chain C: H.255, Q.474, R.477, W.503, V.507 Ligand excluded by PLIP DMS.60: 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.61: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.63: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain C: E.343, H.345, G.349, T.350 Ligand excluded by PLIP DMS.66: 6 residues within 4Å: Chain C: L.83, N.84, G.85, E.86, L.154, F.156 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.70: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.71: 2 residues within 4Å: Chain C: K.650, W.746 Ligand excluded by PLIP DMS.72: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.73: 6 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, N.733 Ligands: NA.58 Ligand excluded by PLIP DMS.74: 6 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain C: S.77, Q.78, L.80, R.81 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: R.259, F.260, N.261, R.266, V.268 Ligand excluded by PLIP DMS.77: 3 residues within 4Å: Chain C: K.840, Y.845, M.997 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain A: D.457, P.459 Chain D: Q.474, R.477 Ligand excluded by PLIP DMS.85: 9 residues within 4Å: Chain D: V.256, T.258, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.86: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.87: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.88: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.96 Ligand excluded by PLIP DMS.89: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.91: 5 residues within 4Å: Chain D: L.83, N.84, E.86, W.87, L.154 Ligand excluded by PLIP DMS.92: 4 residues within 4Å: Chain D: V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain D: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: G.304, G.305, E.306, T.319, R.321 Ligand excluded by PLIP DMS.95: 2 residues within 4Å: Chain D: K.650, W.746 Ligand excluded by PLIP DMS.96: 8 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77, L.80 Ligands: DMS.88 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 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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