SMTL ID : 3t09.1

E. coli (LacZ) beta-galactosidase (S796A) galactonolactone complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

149.1: 14 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, W.1028 Ligands: NA.6, DMS.38 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.131, A:D.230, A:H.420, A:N.489, A:E.490 Water bridges: A:D.230, A:D.230, A:D.230 149.39: 14 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 Ligands: NA.43, DMS.74 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:H.420, B:N.489, B:E.490 Water bridges: B:D.230, B:E.490, B:E.490 149.75: 14 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 Ligands: NA.78, DMS.106 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.420, C:N.489, C:E.490 Water bridges: C:D.230, C:E.490, C:E.490 149.107: 15 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, W.1028 Ligands: NA.110, DMS.137 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.230, D:H.420, D:N.489, D:E.490 Water bridges: D:D.230, D:D.230, D:D.230

11 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

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.40, H2O.41, H2O.41 MG.3: 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.4: 2 residues within 4Å: Chain A: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 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.81, H2O.81, H2O.81 MG.41: 7 residues within 4Å: Chain B: D.44, W.45, 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.42: 1 residues within 4Å: Chain B: Q.747 No protein-ligand interaction detected (PLIP) MG.76: 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.122, H2O.122, H2O.123 MG.77: 7 residues within 4Å: Chain C: D.44, W.45, N.47, V.50, Y.190, 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.108: 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.165, H2O.165, H2O.165 MG.109: 6 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, 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

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

NA.6: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: 149.1 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.8: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: S.676, E.679, L.699 Ligands: DMS.31 Ligand excluded by PLIP NA.43: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: 149.39 Ligand excluded by PLIP NA.44: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.45: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.46: 6 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.66 Ligand excluded by PLIP NA.78: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: 149.75 Ligand excluded by PLIP NA.79: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.80: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.81: 6 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.100 Ligand excluded by PLIP NA.110: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: 149.107 Ligand excluded by PLIP NA.111: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.112: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.113: 6 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.133 Ligand excluded by PLIP

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

DMS.10: 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.11: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, 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: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.33 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: R.534, E.537, P.1030, S.1031, V.1032 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain A: L.83, N.84, G.85, E.86, L.154, F.156 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: I.128, P.135, P.144 Ligands: DMS.22, DMS.27 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.21: 6 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain A: G.622, D.623, T.624 Ligands: DMS.19 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: V.113, V.114, H.122 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: K.650, I.743, W.746 Ligand excluded by PLIP DMS.25: 3 residues within 4Å: Chain A: L.279, R.280, D.281 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain A: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: Y.134, P.135, T.137 Ligands: DMS.19 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: D.457, P.459 Chain D: R.477, V.507 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: D.111, H.122, G.123, Y.124 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain A: Y.955, Y.991, R.1002, L.1005 Ligand excluded by PLIP DMS.31: 6 residues within 4Å: Chain A: D.677, N.678, E.679, P.732, N.733 Ligands: NA.9 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain A: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.33: 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.34: 3 residues within 4Å: Chain A: E.86, L.154, T.155 Ligand excluded by PLIP DMS.35: 3 residues within 4Å: Chain A: F.658, Q.747, W.749 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain A: R.66, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.38: 7 residues within 4Å: Chain A: N.131, V.132, H.447, F.630, A.825, W.1028 Ligands: 149.1 Ligand excluded by PLIP DMS.47: 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.48: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.50: 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.51: 4 residues within 4Å: Chain B: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.53: 6 residues within 4Å: Chain B: L.83, N.84, G.85, E.86, W.87, L.154 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: P.135, P.144, W.220 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain B: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain B: V.113, V.114, H.122 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain B: K.650, R.728, I.743, W.746 Ligand excluded by PLIP DMS.60: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain B: F.260, N.261, D.262, E.363 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain B: T.133, Y.134, P.135 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain B: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.66: 6 residues within 4Å: Chain B: D.677, N.678, E.679, P.732, N.733 Ligands: NA.46 Ligand excluded by PLIP DMS.67: 3 residues within 4Å: Chain B: W.724, Q.748, R.750 Ligand excluded by PLIP DMS.68: 4 residues within 4Å: Chain B: W.65, D.74, R.75, P.76 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain B: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.70: 5 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain B: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.72: 4 residues within 4Å: Chain B: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.73: 2 residues within 4Å: Chain B: Y.434, A.736 Ligand excluded by PLIP DMS.74: 6 residues within 4Å: Chain B: N.131, V.132, F.630, A.825, W.1028 Ligands: 149.39 Ligand excluded by PLIP DMS.82: 10 residues within 4Å: Chain C: T.258, D.358, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.83: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.85: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.102 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain C: E.343, H.345, G.349, T.350 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain C: E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain C: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.91: 5 residues within 4Å: Chain C: I.128, P.135, P.144, W.220 Ligands: DMS.97 Ligand excluded by PLIP DMS.92: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.94: 3 residues within 4Å: Chain C: V.113, V.114, H.122 Ligand excluded by PLIP DMS.95: 3 residues within 4Å: Chain C: K.650, I.743, W.746 Ligand excluded by PLIP DMS.96: 2 residues within 4Å: Chain C: R.280, D.281 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain C: Y.134, P.135, I.136, T.137 Ligands: DMS.91 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.100: 7 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, P.732, N.733 Ligands: NA.81 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain C: W.724, Q.748, R.750 Ligand excluded by PLIP DMS.102: 6 residues within 4Å: Chain C: W.65, D.74, R.75, P.76, S.77 Ligands: DMS.85 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain C: F.658, R.659, L.660, Q.747, W.749 Ligand excluded by PLIP DMS.104: 5 residues within 4Å: Chain C: L.951, S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.105: 6 residues within 4Å: Chain C: W.162, L.163, Q.164, E.165, G.166, S.203 Ligand excluded by PLIP DMS.106: 7 residues within 4Å: Chain C: N.131, V.132, H.447, E.490, A.825, W.1028 Ligands: 149.75 Ligand excluded by PLIP DMS.114: 10 residues within 4Å: Chain D: T.258, D.358, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.115: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.117: 6 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligand excluded by PLIP DMS.118: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: E.343, H.345, T.346, G.349, T.350 Ligand excluded by PLIP DMS.120: 4 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.121: 5 residues within 4Å: Chain D: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain D: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.123: 3 residues within 4Å: Chain D: P.135, P.144, W.220 Ligand excluded by PLIP DMS.124: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.126: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.127: 2 residues within 4Å: Chain D: K.650, W.746 Ligand excluded by PLIP DMS.128: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.129: 5 residues within 4Å: Chain D: F.260, N.261, D.262, F.264, E.363 Ligand excluded by PLIP DMS.130: 4 residues within 4Å: Chain A: W.503, V.507 Chain D: D.457, P.459 Ligand excluded by PLIP DMS.131: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.132: 4 residues within 4Å: Chain D: Y.955, P.957, Y.991, R.1002 Ligand excluded by PLIP DMS.133: 6 residues within 4Å: Chain D: D.677, N.678, E.679, P.732, N.733 Ligands: NA.113 Ligand excluded by PLIP DMS.134: 3 residues within 4Å: Chain D: W.724, Q.748, R.750 Ligand excluded by PLIP DMS.135: 5 residues within 4Å: Chain D: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.136: 5 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991, A.1007 Ligand excluded by PLIP DMS.137: 7 residues within 4Å: Chain D: N.131, V.132, H.447, F.630, A.825, W.1028 Ligands: 149.107 Ligand excluded by PLIP DMS.138: 6 residues within 4Å: Chain D: W.162, L.163, Q.164, E.165, G.166, S.203 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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