SMTL ID : 3t0d.1

E.coli (lacZ) beta-galactosidase (S796T) in complex with galactonolactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-tetramer

Ligands

4 x 149: D-galactonolactone(Non-covalent)

149.1: 15 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, W.1028 Ligands: NA.4, DMS.26 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.230, A:H.420, A:N.489, A:E.490 Water bridges: A:D.230, A:E.490, A:E.490 149.30: 15 residues within 4Å: Chain B: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.34, DMS.60 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.230, B:H.420, B:N.489, B:E.490 Water bridges: B:N.131, B:D.230, B:D.230, B:E.490 149.64: 15 residues within 4Å: Chain C: N.131, D.230, H.420, N.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.67, DMS.98 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:H.420, C:N.489, C:E.490 Water bridges: C:N.131, C:D.230, C:D.230, C:D.230 149.101: 14 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 Ligands: NA.104, DMS.127 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.131, D:D.230, D:H.420, D:N.489, D:E.490 Water bridges: D:D.230, D:E.490, D:E.490

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.3: 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.31: 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.38, H2O.41, H2O.43 MG.32: 6 residues within 4Å: Chain B: D.44, W.45, N.47, V.50, 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.33: 1 residues within 4Å: Chain B: Q.747 No protein-ligand interaction detected (PLIP) MG.65: 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.84, H2O.87 MG.66: 6 residues within 4Å: Chain C: D.44, W.45, N.47, V.50, 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.102: 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.125, H2O.128 MG.103: 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

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

NA.4: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: 149.1 Ligand excluded by PLIP NA.5: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.6: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.34: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: 149.30 Ligand excluded by PLIP NA.35: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.36: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.37: 5 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.67: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: 149.64 Ligand excluded by PLIP NA.68: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.69: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.70: 5 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.104: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: 149.101 Ligand excluded by PLIP NA.105: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.106: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.107: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP

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

DMS.8: 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.9: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 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.22 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: E.363, V.364, P.509, S.510 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: 6 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: V.113, V.114, H.122 Ligand excluded by PLIP DMS.19: 2 residues within 4Å: Chain A: R.280, D.281 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.11 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: R.66, Q.79, W.162, 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: I.766, H.768, E.779, L.780, G.781 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain A: N.131, V.132, F.630, W.1028 Ligands: 149.1 Ligand excluded by PLIP DMS.27: 6 residues within 4Å: Chain A: Q.410, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.28: 6 residues within 4Å: Chain A: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: Y.501, T.523, T.525, D.526 Ligand excluded by PLIP DMS.38: 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.39: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 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: 8 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.59 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: 4 residues within 4Å: Chain B: T.286, E.343, H.345, G.349 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain B: P.135, P.144, W.220 Ligands: DMS.63 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.47: 6 residues within 4Å: Chain B: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: R.477, W.503, V.507 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.53: 6 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain B: S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.57: 3 residues within 4Å: Chain B: I.334, P.335, N.336 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: L.406, T.735, A.736, S.738, E.739 Ligand excluded by PLIP DMS.59: 7 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.41 Ligand excluded by PLIP DMS.60: 6 residues within 4Å: Chain B: N.131, V.132, H.447, E.490, W.1028 Ligands: 149.30 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain B: T.726, R.728, I.743, W.746 Ligand excluded by PLIP DMS.62: 4 residues within 4Å: Chain B: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.63: 7 residues within 4Å: Chain B: T.133, Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.45 Ligand excluded by PLIP DMS.71: 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.72: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.73: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.74: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.88 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.76: 4 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.77: 5 residues within 4Å: Chain C: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain C: I.128, P.135, P.144, W.220 Ligand excluded by PLIP DMS.79: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.81: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.82: 4 residues within 4Å: Chain C: K.650, I.743, W.746 Ligands: DMS.95 Ligand excluded by PLIP DMS.83: 2 residues within 4Å: Chain C: R.280, D.281 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain C: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.85: 3 residues within 4Å: Chain B: V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.86: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain C: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.88: 7 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.74 Ligand excluded by PLIP DMS.89: 3 residues within 4Å: Chain C: Q.295, V.296, A.297 Ligand excluded by PLIP DMS.90: 6 residues within 4Å: Chain C: E.86, W.87, R.88, S.153, L.154, T.155 Ligand excluded by PLIP DMS.91: 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.92: 3 residues within 4Å: Chain C: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain C: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.95: 6 residues within 4Å: Chain C: T.726, R.728, I.743, W.746, C.943 Ligands: DMS.82 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain C: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: P.135, T.137, P.625 Ligand excluded by PLIP DMS.98: 7 residues within 4Å: Chain C: N.131, V.132, H.447, E.490, F.630, W.1028 Ligands: 149.64 Ligand excluded by PLIP DMS.99: 5 residues within 4Å: Chain C: Y.501, T.523, T.525, D.526, R.560 Ligand excluded by PLIP DMS.100: 1 residues within 4Å: Chain C: Y.607 Ligand excluded by PLIP DMS.108: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.109: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.110: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.123 Ligand excluded by PLIP DMS.111: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.112: 5 residues within 4Å: Chain D: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.113: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.114: 4 residues within 4Å: Chain D: P.135, P.144, E.146 Ligands: DMS.120 Ligand excluded by PLIP DMS.115: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain D: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.117: 3 residues within 4Å: Chain D: V.113, V.114, H.122 Ligand excluded by PLIP DMS.118: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.120: 7 residues within 4Å: Chain D: T.133, Y.134, P.135, I.136, T.137, P.625 Ligands: DMS.114 Ligand excluded by PLIP DMS.121: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain D: Y.955, Y.991, R.1002, L.1005 Ligand excluded by PLIP DMS.123: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.110 Ligand excluded by PLIP DMS.124: 3 residues within 4Å: Chain D: F.658, Q.747, W.749 Ligand excluded by PLIP DMS.125: 4 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.126: 5 residues within 4Å: Chain D: L.163, Q.164, E.165, G.166, S.203 Ligand excluded by PLIP DMS.127: 4 residues within 4Å: Chain D: N.131, F.630, W.1028 Ligands: 149.101 Ligand excluded by PLIP DMS.128: 5 residues within 4Å: Chain D: I.766, H.768, E.779, L.780, G.781 Ligand excluded by PLIP DMS.129: 2 residues within 4Å: Chain D: K.650, W.746 Ligand excluded by PLIP DMS.130: 4 residues within 4Å: Chain D: R.659, S.661, T.664, E.666 Ligand excluded by PLIP DMS.131: 1 residues within 4Å: Chain D: R.750 Ligand excluded by PLIP DMS.132: 5 residues within 4Å: Chain D: W.724, Q.747, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.133: 6 residues within 4Å: Chain D: L.406, Q.410, A.736, W.737, S.738, E.739 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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