SMTL ID : 4duv.1

E. coli (lacZ) beta-galactosidase (G974A) 2-deoxy-galactosyl-enzyme and bis-Tris complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x 2DG: 2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

2DG.1: 12 residues within 4Å: Chain A: D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.131, A:D.230, A:H.420, A:N.489 Water bridges: A:D.230, A:D.230, A:D.230 2DG.28: 12 residues within 4Å: Chain B: D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.33 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.131, B:D.230, B:H.420, B:N.489 Water bridges: B:D.230, B:D.230, B:D.230 2DG.61: 12 residues within 4Å: Chain C: D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.65 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.131, C:H.420, C:N.489, C:Y.532, C:H.569 Water bridges: C:D.230, C:D.230, C:D.230 2DG.94: 12 residues within 4Å: Chain D: D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.98 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.420, D:N.489, D:Y.532 Water bridges: D:D.230, D:D.230, D:D.230

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.2: 11 residues within 4Å: Chain A: N.131, V.132, H.447, M.452, E.490, F.630, S.825, E.826, R.829, W.1028 Chain D: E.310 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.131, A:N.131, A:E.826 Water bridges: A:D.230, A:E.490, A:E.826, A:W.1028 pi-Cation interactions: A:W.1028 BTB.29: 10 residues within 4Å: Chain B: N.131, V.132, H.447, E.490, F.630, S.825, E.826, R.829, W.1028 Chain C: E.310 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.131, B:N.131, B:E.490, B:S.825, B:E.826, B:E.826 Water bridges: B:D.230, B:E.826, B:W.1028 pi-Cation interactions: B:W.1028 BTB.62: 10 residues within 4Å: Chain B: E.310 Chain C: N.131, V.132, H.447, M.452, E.490, F.630, S.825, E.826, W.1028 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.131, C:N.131, C:E.490, C:S.825, C:E.826 Water bridges: C:E.826, C:W.1028 BTB.95: 10 residues within 4Å: Chain A: E.310 Chain D: N.131, V.132, H.447, M.452, E.490, F.630, S.825, E.826, W.1028 10 PLIP interactions: 9 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.131, D:N.131, D:S.825, D:E.826 Water bridges: D:E.490, D:E.826, D:W.1028, D:W.1028, A:E.310 pi-Cation interactions: D:W.1028

9 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 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.38, H2O.38, H2O.39 MG.4: 5 residues within 4Å: Chain A: D.44, N.47, V.50, 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.30: 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.47, H2O.75, H2O.76 MG.31: 6 residues within 4Å: Chain B: D.44, 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.32: 2 residues within 4Å: Chain B: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.63: 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.112, H2O.114, H2O.114 MG.64: 5 residues within 4Å: Chain C: D.44, 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.96: 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.118, H2O.124, H2O.151 MG.97: 5 residues within 4Å: Chain D: D.44, N.47, V.50, 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

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

NA.5: 6 residues within 4Å: Chain A: Y.129, D.230, W.597, F.630, N.633 Ligands: 2DG.1 Ligand excluded by PLIP NA.6: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain A: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.33: 6 residues within 4Å: Chain B: Y.129, D.230, W.597, F.630, N.633 Ligands: 2DG.28 Ligand excluded by PLIP NA.34: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.35: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.36: 4 residues within 4Å: Chain B: S.676, N.678, E.679, L.699 Ligand excluded by PLIP NA.65: 6 residues within 4Å: Chain C: Y.129, D.230, W.597, F.630, N.633 Ligands: 2DG.61 Ligand excluded by PLIP NA.66: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.67: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.68: 5 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.98: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: 2DG.94 Ligand excluded by PLIP NA.99: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.100: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.101: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP

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

DMS.9: 4 residues within 4Å: Chain A: D.457, P.459 Chain D: R.477, V.507 Ligand excluded by PLIP DMS.10: 8 residues within 4Å: Chain A: T.258, V.359, G.360, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.11: 7 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, F.656, Q.657, Q.747 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.13: 7 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.22 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: Y.134, P.135, I.136, T.137, P.625 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.22: 7 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.13 Ligand excluded by PLIP DMS.23: 6 residues within 4Å: Chain A: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.25: 5 residues within 4Å: Chain A: R.259, F.260, N.261, R.266, A.267 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: Y.501, T.523, T.525, R.560 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain A: L.406, T.735, A.736, S.738, E.739 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: Y.501, T.523, T.525, D.526 Ligands: DMS.38 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain B: G.557, E.558, T.559, R.560 Ligands: DMS.37 Ligand excluded by PLIP DMS.39: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.41: 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.42: 4 residues within 4Å: Chain B: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.45: 5 residues within 4Å: Chain B: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain B: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain B: D.457, P.459 Chain C: R.477, V.507 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain B: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.51: 6 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain B: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: I.334, P.335, N.336 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: T.735, A.736, S.738, E.739 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: Y.134, P.135, I.136, T.137, P.625 Ligand excluded by PLIP DMS.57: 6 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, P.76, S.77 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: R.259, F.260, N.261, R.266, V.268 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain B: S.82, L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.60: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain C: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.70: 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.71: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.73: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.84 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.77: 6 residues within 4Å: Chain C: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.79: 3 residues within 4Å: Chain C: K.650, I.743, W.746 Ligand excluded by PLIP DMS.80: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.81: 2 residues within 4Å: Chain B: V.507 Chain C: D.457 Ligand excluded by PLIP DMS.82: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.83: 4 residues within 4Å: Chain C: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.84: 7 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.73 Ligand excluded by PLIP DMS.85: 5 residues within 4Å: Chain C: Y.134, P.135, I.136, T.137, P.625 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain C: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.87: 7 residues within 4Å: Chain C: L.406, Q.410, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.88: 2 residues within 4Å: Chain C: R.433, Y.434 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.90: 6 residues within 4Å: Chain C: Y.501, T.522, T.523, T.525, D.526, R.560 Ligand excluded by PLIP DMS.91: 5 residues within 4Å: Chain C: L.83, N.84, E.86, L.154, F.156 Ligand excluded by PLIP DMS.92: 5 residues within 4Å: Chain C: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain C: M.121, I.605, F.621 Ligand excluded by PLIP DMS.102: 4 residues within 4Å: Chain D: Q.120, M.121, I.605, F.621 Ligand excluded by PLIP DMS.103: 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.104: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.106: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.117 Ligand excluded by PLIP DMS.107: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.108: 4 residues within 4Å: Chain D: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.109: 4 residues within 4Å: Chain D: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.110: 4 residues within 4Å: Chain D: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.111: 5 residues within 4Å: Chain D: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.112: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.113: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.114: 3 residues within 4Å: Chain D: Y.134, P.135, T.137 Ligand excluded by PLIP DMS.115: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.116: 4 residues within 4Å: Chain D: Y.955, Y.991, R.1002 Ligands: DMS.119 Ligand excluded by PLIP DMS.117: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.106 Ligand excluded by PLIP DMS.118: 5 residues within 4Å: Chain D: F.658, R.659, L.660, Q.747, W.749 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991 Ligands: DMS.116 Ligand excluded by PLIP DMS.120: 5 residues within 4Å: Chain D: W.162, L.163, Q.164, G.166, S.203 Ligand excluded by PLIP DMS.121: 3 residues within 4Å: Chain D: K.650, I.743, W.746 Ligand excluded by PLIP DMS.122: 5 residues within 4Å: Chain D: Q.410, T.735, W.737, S.738, E.739 Ligand excluded by PLIP DMS.123: 4 residues within 4Å: Chain D: R.259, F.260, N.261, V.268 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wheatley, R.W. et al., The Glucose Acceptor site of lacZ beta-galactosidase for the synthesis of allolactose - the natural inducer of the lac operon. To be Published

Release Date

2013-04-03

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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