SMTL ID : 4duw.1

E. coli (lacZ) beta-galactosidase (G974A) in complex with allolactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x BGC- GAL: beta-D-galactopyranose-(1-6)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.1: 16 residues within 4Å: Chain A: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, S.825, E.826, W.1028 Ligands: NA.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.131, A:S.825, A:S.825, A:H.420, A:N.489, A:E.490 Salt bridges: A:H.447 Water bridges: A:D.230, A:D.230, A:D.230 BGC-GAL.2: 18 residues within 4Å: Chain B: N.131, V.132, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, S.825, E.826, R.829, W.1028 Ligands: NA.33 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.131, B:S.825, B:E.826, B:E.826, B:R.829, B:D.230, B:H.420, B:N.489, B:E.490 Water bridges: B:H.447, B:H.447, B:D.230, B:D.230, B:D.230 Salt bridges: B:H.447 BGC-GAL.3: 17 residues within 4Å: Chain C: N.131, V.132, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, S.825, E.826, W.1028 Ligands: NA.63 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.131, C:S.825, C:E.826, C:H.420, C:N.489, C:E.490, C:Y.532 Water bridges: C:E.490, C:D.230, C:D.230, C:D.230 Salt bridges: C:H.447 BGC-GAL.4: 17 residues within 4Å: Chain D: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, S.825, E.826, W.1028 Ligands: MG.87, NA.89 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.131, D:E.490, D:S.825, D:S.825, D:D.230, D:H.420, D:N.489, D:E.490, D:Y.532 Water bridges: D:D.230, D:H.447, D:N.131, D:D.230, D:D.230, D:D.230 Salt bridges: D:H.447

10 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 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.1, H2O.3, H2O.6 MG.6: 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.7: 2 residues within 4Å: Chain A: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain B: N.131, D.230, 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.36, H2O.39 MG.31: 5 residues within 4Å: Chain B: D.44, 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.32: 1 residues within 4Å: Chain B: E.398 No protein-ligand interaction detected (PLIP) MG.61: 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.72, H2O.75, H2O.78 MG.62: 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.87: 5 residues within 4Å: Chain D: N.131, E.445, H.447, E.490 Ligands: BGC-GAL.4 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.445, D:H.447, D:E.490, H2O.110, H2O.112, H2O.115 MG.88: 6 residues within 4Å: Chain D: D.44, 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

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

NA.8: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: BGC-GAL.1 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.10: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.11: 5 residues within 4Å: Chain A: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: BGC-GAL.2 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: 5 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.63: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: BGC-GAL.3 Ligand excluded by PLIP NA.64: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.65: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.66: 4 residues within 4Å: Chain C: S.676, D.677, E.679, L.699 Ligand excluded by PLIP NA.89: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: BGC-GAL.4 Ligand excluded by PLIP NA.90: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.91: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.92: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP

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

DMS.12: 7 residues within 4Å: Chain A: T.258, V.359, G.360, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.15: 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.16: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: V.364, R.365, P.509 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain A: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.24: 6 residues within 4Å: Chain A: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: Y.501, T.523, T.525, R.560 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain A: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: L.83, N.84, W.87, L.154 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain A: Q.812, F.813, T.814, H.844, W.871 Ligand excluded by PLIP DMS.29: 3 residues within 4Å: Chain A: D.904 Chain B: R.750, L.751 Ligand excluded by PLIP DMS.37: 9 residues within 4Å: Chain B: V.256, T.258, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.38: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.40: 7 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.57 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain B: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain B: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain B: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.44: 3 residues within 4Å: Chain B: P.135, P.144 Ligands: DMS.56 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain B: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.46: 6 residues within 4Å: Chain B: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain B: L.279, R.280, D.281 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: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 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: 5 residues within 4Å: Chain B: E.398, L.426, L.430, R.433 Ligands: DMS.53 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain B: R.433, Y.434 Ligands: DMS.52 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: I.334, P.335, N.336 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: Q.410, T.735, W.737, S.738, E.739 Ligand excluded by PLIP DMS.56: 6 residues within 4Å: Chain B: Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.44 Ligand excluded by PLIP DMS.57: 7 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.40 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: L.83, N.84, E.86, L.154, F.156 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain B: Y.501, T.523, T.525, D.526, R.560 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: T.73, D.74, R.75, P.76 Ligand excluded by PLIP DMS.67: 9 residues within 4Å: Chain C: V.256, T.258, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.68: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.70: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.82 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.72: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.73: 4 residues within 4Å: Chain C: I.128, P.135, P.144, W.220 Ligand excluded by PLIP DMS.74: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.75: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.76: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.77: 2 residues within 4Å: Chain C: K.650, W.746 Ligand excluded by PLIP DMS.78: 2 residues within 4Å: Chain C: R.280, D.281 Ligand excluded by PLIP DMS.79: 3 residues within 4Å: Chain B: Q.474 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.80: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.81: 4 residues within 4Å: Chain C: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.82: 7 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.70 Ligand excluded by PLIP DMS.83: 5 residues within 4Å: Chain C: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.84: 6 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.85: 6 residues within 4Å: Chain C: S.82, L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.86: 6 residues within 4Å: Chain C: E.86, W.87, R.88, S.153, L.154, T.155 Ligand excluded by PLIP DMS.93: 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.94: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.96: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.104 Ligand excluded by PLIP DMS.97: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.98: 5 residues within 4Å: Chain D: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.99: 3 residues within 4Å: Chain D: E.363, V.364, P.509 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain D: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.101: 6 residues within 4Å: Chain D: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.102: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.103: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.104: 6 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76 Ligands: DMS.96 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain D: T.726, R.728, I.743, W.746, C.943 Ligand excluded by PLIP DMS.106: 6 residues within 4Å: Chain D: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.107: 4 residues within 4Å: Chain D: L.83, N.84, W.87, L.154 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wheatley, R.W. et al., Structural Explanation for Allolactose (lac operon inducer) Synthesis by lacZ beta-Galactosidase and the Evolutionary Relationship between Allolactose synthesis and the lac Repressor. J.Biol.Chem. (2013)

Release Date

2013-03-20

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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