SMTL ID : 4dux.1

E. coli (lacZ) beta-galactosidase (N460S) in complex with L-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

9 x 0MK: beta-L-ribopyranose(Non-covalent)

0MK.1: 12 residues within 4Å: Chain A: D.230, H.420, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: 0MK.2, NA.5 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.420, A:N.633 Water bridges: A:D.230, A:D.230, A:H.420, A:H.420, A:S.489 0MK.2: 9 residues within 4Å: Chain A: N.131, V.132, H.447, E.490, M.531, S.825, E.826, W.1028 Ligands: 0MK.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.131, A:S.825, A:E.826, A:E.826 Water bridges: A:E.490 Salt bridges: A:H.447 0MK.26: 14 residues within 4Å: Chain B: N.131, D.230, H.420, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: 0MK.27, NA.31 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:H.420, B:N.633 Water bridges: B:N.131, B:D.230, B:D.230, B:R.417, B:H.420, B:H.420, B:E.445 0MK.27: 10 residues within 4Å: Chain B: N.131, V.132, H.447, E.490, M.531, F.630, S.825, E.826, W.1028 Ligands: 0MK.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.131, B:S.825, B:S.825, B:E.826, B:E.826 Salt bridges: B:H.447 0MK.28: 5 residues within 4Å: Chain B: P.817, V.836, E.837, K.840 Ligands: DMS.47 3 PLIP interactions: 3 interactions with chain B Water bridges: B:M.997, B:M.997 Salt bridges: B:K.840 0MK.49: 14 residues within 4Å: Chain C: N.131, D.230, H.420, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: 0MK.50, NA.53 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.230, C:H.420, C:E.490, C:Y.532, C:N.633 Water bridges: C:N.131, C:D.230, C:D.230, C:R.417, C:H.420, C:E.490 0MK.50: 9 residues within 4Å: Chain C: N.131, V.132, E.490, M.531, F.630, S.825, E.826, W.1028 Ligands: 0MK.49 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.131, C:S.825, C:E.826, C:E.826 Water bridges: C:E.490, C:E.490 Salt bridges: C:H.447 0MK.72: 14 residues within 4Å: Chain D: N.131, D.230, H.420, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: 0MK.73, NA.76 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:D.230, D:H.420, D:Y.532, D:N.633 Water bridges: D:N.131, D:D.230, D:D.230, D:D.230, D:R.417, D:H.420, D:H.420, D:H.447 0MK.73: 9 residues within 4Å: Chain D: N.131, V.132, H.447, E.490, M.531, S.825, E.826, W.1028 Ligands: 0MK.72 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.131, D:S.825 Water bridges: D:E.490 Salt bridges: D:H.447

8 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.6, H2O.25, H2O.25 MG.4: 5 residues within 4Å: Chain A: D.44, N.47, V.50, Q.192, D.222 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.44, A:N.47, A:V.50, A:D.222, A:D.222 MG.29: 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.28, H2O.33, H2O.49 MG.30: 6 residues within 4Å: Chain B: D.44, 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.51: 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.74, H2O.74, H2O.74 MG.52: 6 residues within 4Å: Chain C: D.44, 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.74: 4 residues within 4Å: Chain D: N.131, 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.82, H2O.101, H2O.101 MG.75: 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

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

NA.5: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: 0MK.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.630, A:N.633 NA.6: 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:L.591 NA.7: 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.31: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: 0MK.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230, B:N.633 NA.32: 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:Y.588 NA.33: 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:T.999 NA.34: 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.53: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: 0MK.49 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.129, C:D.230, C:N.633 NA.54: 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.55: 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.56: 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:S.676, C:E.679 NA.76: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: 0MK.72 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.129, D:D.230, D:N.633 NA.77: 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.78: 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:T.999

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

DMS.8: 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.9: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, F.656, Q.657 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.11: 7 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.19 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: S.82, L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: I.128, P.135, I.136, P.144 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: G.304, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: A.63, P.76, L.80 Ligands: DMS.11 Ligand excluded by PLIP DMS.20: 6 residues within 4Å: Chain A: E.86, W.87, R.88, S.153, L.154, T.155 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.23: 6 residues within 4Å: Chain A: Q.410, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.24: 2 residues within 4Å: Chain A: T.523, T.525 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.35: 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.36: 4 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.657 Ligand excluded by PLIP DMS.37: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.38: 8 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.44 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.40: 3 residues within 4Å: Chain B: L.83, N.84, L.154 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain B: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain B: D.457, P.459 Chain C: W.503, V.507 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: A.63, W.65, D.74, R.75 Ligands: DMS.38 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain B: E.86, W.87, R.88, S.153, L.154, T.155 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain B: S.161, W.162, H.245 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: P.817, V.836, Y.845, M.997 Ligands: 0MK.28 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain B: L.279, D.316 Chain C: R.454 Ligand excluded by PLIP DMS.57: 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.58: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.60: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.68 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain C: S.82, L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.64: 2 residues within 4Å: Chain C: E.363, V.364 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.66: 3 residues within 4Å: Chain C: V.318, T.319, R.321 Ligand excluded by PLIP DMS.67: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain C: A.63, W.65, R.75, P.76 Ligands: DMS.60 Ligand excluded by PLIP DMS.69: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.70: 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.71: 6 residues within 4Å: Chain C: F.260, N.261, D.262, F.264, E.363, R.365 Ligand excluded by PLIP DMS.79: 8 residues within 4Å: Chain D: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.81: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.82: 7 residues within 4Å: Chain D: F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.90 Ligand excluded by PLIP DMS.83: 4 residues within 4Å: Chain D: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.84: 4 residues within 4Å: Chain D: E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.85: 4 residues within 4Å: Chain D: S.82, L.83, N.84, L.154 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain D: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.87: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.88: 3 residues within 4Å: Chain D: V.318, T.319, R.321 Ligand excluded by PLIP DMS.89: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.90: 6 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76 Ligands: DMS.82 Ligand excluded by PLIP DMS.91: 5 residues within 4Å: Chain A: R.311, G.312, G.313, A.315 Chain D: V.450 Ligand excluded by PLIP DMS.92: 4 residues within 4Å: Chain D: R.259, F.260, N.261, V.268 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain D: Y.501, T.523, T.525, R.560 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.95: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.96: 5 residues within 4Å: Chain D: P.817, V.836, K.840, Y.845, M.997 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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