SMTL ID : 3t2p.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

IPT.1: 12 residues within 4Å: Chain A: N.131, D.230, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.4 9 PLIP interactions: 9 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:N.489, A:E.490, A:E.566 IPT.21: 13 residues within 4Å: Chain B: N.131, D.230, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, V.824, W.1028 Ligands: NA.24 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.824, B:W.1028 Hydrogen bonds: B:N.131, B:D.230, B:E.490, B:F.630, B:N.633 IPT.41: 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.44 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:D.230, C:E.490 IPT.65: 12 residues within 4Å: Chain D: N.131, D.230, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.68 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:H.447, D:N.489, D:N.489, D:E.490, D:E.490, D:E.490

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.445, H.447, E.490 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.445, A:H.447, A:E.490, H2O.2, H2O.14 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.22: 3 residues within 4Å: Chain B: E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.447, B:E.490, H2O.23, H2O.23, H2O.24 MG.23: 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.35, H2O.36, H2O.36 MG.43: 7 residues within 4Å: Chain C: D.44, W.45, N.47, V.50, Y.190, 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.66: 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.38, H2O.41, H2O.49 MG.67: 7 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.44, D:N.47, D:V.50, D:D.222, D:D.222

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

NA.4: 7 residues within 4Å: Chain A: Y.129, D.230, W.597, F.630, C.631, N.633 Ligands: IPT.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.230, A:N.633 NA.5: 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:F.585 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:L.996 NA.24: 6 residues within 4Å: Chain B: Y.129, D.230, W.597, F.630, N.633 Ligands: IPT.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.597, B:N.633 NA.25: 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.44: 6 residues within 4Å: Chain C: Y.129, D.230, F.630, C.631, N.633 Ligands: IPT.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 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.589 NA.46: 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:L.699 NA.68: 6 residues within 4Å: Chain D: Y.129, D.230, W.597, F.630, N.633 Ligands: IPT.65 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.129, D:N.633, D:N.633 NA.69: 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

63 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, R.339, A.356 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.12: 6 residues within 4Å: Chain A: S.82, L.83, N.84, W.87, L.154, F.156 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: 4 residues within 4Å: Chain A: G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: D.457, P.459, A.495 Chain D: Q.474, 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: 5 residues within 4Å: Chain A: E.86, R.88, S.153, L.154, T.155 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: R.311, G.312, G.313, A.315 Chain D: V.450 Ligand excluded by PLIP DMS.26: 9 residues within 4Å: Chain B: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain B: K.409, N.412, 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: 3 residues within 4Å: Chain B: G.299, L.320, R.321 Ligand excluded by PLIP DMS.31: 5 residues within 4Å: Chain B: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain B: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain B: S.82, L.83, N.84, L.154, T.155, F.156 Ligand excluded by PLIP DMS.34: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain B: I.605, P.613, W.614, S.615 Ligand excluded by PLIP DMS.36: 4 residues within 4Å: Chain B: G.304, V.318, T.319, R.321 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain B: D.111, H.122, G.123, Y.124 Ligand excluded by PLIP DMS.39: 6 residues within 4Å: Chain B: W.65, D.74, R.75, P.76, L.80 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: 8 residues within 4Å: Chain C: T.258, V.359, G.360, R.362, R.477, N.478, 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.63 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain C: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain C: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain C: S.82, L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain C: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain C: I.128, P.135, I.136 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.60: 3 residues within 4Å: Chain C: K.650, I.743, W.746 Ligand excluded by PLIP DMS.61: 5 residues within 4Å: Chain B: Q.474, W.503, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain C: D.74, P.76, L.80 Ligands: DMS.50 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain C: F.658, R.659, W.749 Ligand excluded by PLIP DMS.70: 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.71: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.73: 8 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.84 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.75: 5 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.76: 4 residues within 4Å: Chain D: L.83, N.84, W.87, L.154 Ligand excluded by PLIP DMS.77: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.78: 2 residues within 4Å: Chain D: P.135, W.220 Ligand excluded by PLIP DMS.79: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain D: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.81: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.82: 4 residues within 4Å: Chain D: K.650, R.728, I.743, W.746 Ligand excluded by PLIP DMS.83: 6 residues within 4Å: Chain D: F.260, N.261, D.262, F.264, E.363, R.365 Ligand excluded by PLIP DMS.84: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, L.80 Ligands: DMS.73 Ligand excluded by PLIP DMS.85: 5 residues within 4Å: Chain D: Y.501, T.523, T.525, D.526, R.560 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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