SMTL ID : 3sep.1

E. coli (lacZ) beta-galactosidase (S796A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 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.6, H2O.31, H2O.33 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: 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.37, H2O.73, H2O.75 MG.28: 6 residues within 4Å: Chain B: D.44, W.45, N.47, V.50, 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.57: 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.81, H2O.116, H2O.118 MG.58: 6 residues within 4Å: Chain C: D.44, W.45, N.47, V.50, 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.84: 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.123, H2O.129, H2O.156 MG.85: 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: 4 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.630, A:N.633 Water bridges: A:D.230, A:D.230 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:L.996 NA.30: 4 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.230, B:N.633 Water bridges: B:D.230, B:D.230 NA.31: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.588, B:L.591 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.33: 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.59: 4 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.129, C:Y.129, C:N.633 Water bridges: C:D.230, C:D.230 NA.60: 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:F.585, C:L.591 NA.61: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:L.996 NA.62: 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.86: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Y.129, D:D.230, D:N.633 Water bridges: D:D.230, D:D.230 NA.87: 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.88: 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:M.997

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

DMS.6: 9 residues within 4Å: Chain A: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.7: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.9: 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.10: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: R.534, E.537, P.1030, S.1031, V.1032, Q.1037 Ligand excluded by PLIP DMS.12: 6 residues within 4Å: Chain A: L.83, N.84, G.85, E.86, L.154, F.156 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: 3 residues within 4Å: Chain A: P.135, P.144 Ligands: DMS.17 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: Y.134, I.136, T.137, P.625 Ligands: DMS.14 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.9 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: E.86, W.87, 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: 5 residues within 4Å: Chain A: R.259, F.260, N.261, R.266, V.268 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: W.547, L.555 Chain B: P.589 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain A: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.34: 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.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, R.339, A.356 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: 4 residues within 4Å: Chain B: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.40: 6 residues within 4Å: Chain B: L.83, N.84, G.85, 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: 6 residues within 4Å: Chain B: I.128, P.135, I.136, P.144 Ligands: DMS.45, DMS.54 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: 5 residues within 4Å: Chain B: G.304, G.305, 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: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: A.63, W.65, R.75, P.76, L.80 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: 6 residues within 4Å: Chain B: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.51: 3 residues within 4Å: Chain B: T.73, D.74, R.75 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain B: F.1018, A.1040, R.1042, Y.1043, H.1044 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain B: F.658, R.659, L.660, Q.747, W.749 Ligand excluded by PLIP DMS.54: 6 residues within 4Å: Chain B: Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.42 Ligand excluded by PLIP DMS.55: 2 residues within 4Å: Chain B: P.335, N.336 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: R.66, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.63: 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.64: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, F.656, Q.657 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.66: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.78 Ligand excluded by PLIP DMS.67: 5 residues within 4Å: Chain C: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain C: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.69: 6 residues within 4Å: Chain C: S.82, L.83, N.84, W.87, L.154, F.156 Ligand excluded by PLIP DMS.70: 4 residues within 4Å: Chain C: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain C: I.128, P.135, I.136, W.220 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.73: 6 residues within 4Å: Chain C: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.74: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.75: 3 residues within 4Å: Chain C: K.650, I.743, W.746 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain B: Q.474, W.503, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.77: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain C: W.65, D.74, P.76 Ligands: DMS.66 Ligand excluded by PLIP DMS.79: 4 residues within 4Å: Chain C: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain C: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.81: 6 residues within 4Å: Chain C: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.82: 6 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.83: 6 residues within 4Å: Chain A: D.457, P.459 Chain D: Q.474, R.477, W.503, V.507 Ligand excluded by PLIP DMS.89: 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.90: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.91: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.92: 8 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.101 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain D: G.299, T.300, R.321 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain D: S.82, L.83, N.84, W.87, L.154 Ligand excluded by PLIP DMS.96: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.98: 4 residues within 4Å: Chain D: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.99: 3 residues within 4Å: Chain D: V.113, V.114, H.122 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain D: K.650, R.728, I.743, W.746 Ligand excluded by PLIP DMS.101: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.92 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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