SMTL ID : 3t0a.1

E. coli (LacZ) beta-galactosidase (S796T)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.27, H2O.29, H2O.33 MG.2: 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.3: 1 residues within 4Å: Chain A: Q.747 No protein-ligand interaction detected (PLIP) 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.67, H2O.69, H2O.71 MG.32: 7 residues within 4Å: Chain B: D.44, W.45, 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.33: 2 residues within 4Å: Chain B: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.70: 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.106, H2O.108, H2O.109 MG.71: 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.72: 2 residues within 4Å: Chain C: Q.747, T.940 No protein-ligand interaction detected (PLIP) MG.109: 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.136, H2O.140, H2O.143 MG.110: 7 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, Y.190, 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 MG.111: 3 residues within 4Å: Chain D: H.651, Q.747, T.940 No protein-ligand interaction detected (PLIP)

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

NA.4: 4 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 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: 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.37: 4 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.73: 5 residues within 4Å: Chain C: Y.129, D.230, W.597, F.630, N.633 Ligand excluded by PLIP NA.74: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.75: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.76: 6 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.92 Ligand excluded by PLIP NA.112: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligand excluded by PLIP NA.113: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.114: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 Ligand excluded by PLIP NA.115: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP NA.116: 1 residues within 4Å: Chain D: N.626 Ligand excluded by PLIP

110 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: 6 residues within 4Å: Chain A: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.11: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.21 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: 6 residues within 4Å: Chain A: T.286, E.343, H.345, G.349, L.351 Ligands: DMS.30 Ligand excluded by PLIP DMS.14: 6 residues within 4Å: Chain A: R.534, E.537, P.1030, S.1031, V.1032, Q.1037 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: I.128, P.135, P.144, W.220 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: 6 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: L.279, R.280, D.281 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: D.457 Chain D: R.477, V.507 Ligand excluded by PLIP DMS.21: 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.22: 4 residues within 4Å: Chain A: R.66, Q.79, W.162, H.245 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: 4 residues within 4Å: Chain A: Y.501, T.523, T.525, R.560 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.26: 3 residues within 4Å: Chain A: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.27: 6 residues within 4Å: Chain A: Q.812, F.813, T.814, H.844, Y.845, W.871 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain A: D.263, L.329, N.374 Ligand excluded by PLIP DMS.29: 3 residues within 4Å: Chain A: K.650, I.743, W.746 Ligand excluded by PLIP DMS.30: 3 residues within 4Å: Chain A: D.348, G.349 Ligands: DMS.13 Ligand excluded by PLIP DMS.38: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.362, R.477, N.478, 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: 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: 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: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, P.76, S.77 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: P.135, P.144, W.220 Ligands: DMS.50, DMS.68 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain B: G.622, D.623, T.624 Ligands: DMS.47 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: K.650, R.728, I.743, W.746 Ligand excluded by PLIP DMS.53: 2 residues within 4Å: Chain B: R.280, D.281 Ligand excluded by PLIP DMS.54: 6 residues within 4Å: Chain B: F.260, N.261, D.262, F.264, E.363 Chain D: D.262 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: D.457, P.459 Chain C: W.503 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: W.724, Q.748, R.750 Ligand excluded by PLIP DMS.57: 3 residues within 4Å: Chain B: S.161, W.162, H.245 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: S.952, Y.955, R.990, Y.991, A.1007 Ligand excluded by PLIP DMS.59: 1 residues within 4Å: Chain B: Y.434 Ligand excluded by PLIP DMS.60: 6 residues within 4Å: Chain B: L.406, Q.410, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.61: 6 residues within 4Å: Chain B: F.89, A.90, W.91, E.109, D.111, Y.124 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain B: I.334, P.335, N.336 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain B: Y.501, T.523, T.525, D.526 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain B: D.111, H.122, G.123, Y.124 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain B: R.186, A.204, F.205, L.206 Ligand excluded by PLIP DMS.66: 2 residues within 4Å: Chain B: N.84, D.240 Ligand excluded by PLIP DMS.67: 5 residues within 4Å: Chain B: R.259, F.260, N.261, R.266, V.268 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: Y.134, P.135, I.136, T.137 Ligands: DMS.47 Ligand excluded by PLIP DMS.69: 3 residues within 4Å: Chain B: Y.955, Y.991, R.1002 Ligand excluded by PLIP DMS.77: 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.78: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.79: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.80: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.94 Ligand excluded by PLIP DMS.81: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.82: 4 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.83: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.85: 6 residues within 4Å: Chain C: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.87: 2 residues within 4Å: Chain C: K.650, W.746 Ligand excluded by PLIP DMS.88: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: Y.134, P.135, I.136, T.137, P.625 Ligand excluded by PLIP DMS.90: 4 residues within 4Å: Chain B: R.477, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.92: 6 residues within 4Å: Chain C: D.677, N.678, E.679, P.732, N.733 Ligands: NA.76 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain C: W.724, Q.748, R.750 Ligand excluded by PLIP DMS.94: 7 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.80 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain C: E.86, W.87, R.88, T.155 Ligand excluded by PLIP DMS.96: 6 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.97: 2 residues within 4Å: Chain C: P.335, N.336 Ligand excluded by PLIP DMS.98: 4 residues within 4Å: Chain C: P.76, S.77, L.80, R.81 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: Y.501, T.523, T.525, D.526 Ligand excluded by PLIP DMS.100: 6 residues within 4Å: Chain C: L.406, Q.410, T.735, A.736, W.737, S.738 Ligand excluded by PLIP DMS.101: 6 residues within 4Å: Chain C: F.89, A.90, W.91, E.109, D.111, Y.124 Ligand excluded by PLIP DMS.102: 5 residues within 4Å: Chain C: R.259, F.260, N.261, R.266, V.268 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain B: V.450 Chain C: R.311, G.312, G.313, A.315 Ligand excluded by PLIP DMS.104: 3 residues within 4Å: Chain B: V.132, H.447 Chain C: R.311 Ligand excluded by PLIP DMS.105: 4 residues within 4Å: Chain C: I.128, P.135, P.144, W.220 Ligand excluded by PLIP DMS.106: 3 residues within 4Å: Chain C: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.107: 7 residues within 4Å: Chain C: D.811, Q.812, F.813, T.814, H.844, Y.845, W.871 Ligand excluded by PLIP DMS.108: 3 residues within 4Å: Chain C: Q.295, V.296, A.297 Ligand excluded by PLIP DMS.117: 10 residues within 4Å: Chain D: V.256, T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.118: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.120: 7 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.130 Ligand excluded by PLIP DMS.121: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.122: 5 residues within 4Å: Chain D: T.286, E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.123: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.124: 2 residues within 4Å: Chain D: P.135, P.144 Ligand excluded by PLIP DMS.125: 6 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, D.639, R.1002 Ligand excluded by PLIP DMS.126: 6 residues within 4Å: Chain D: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.127: 3 residues within 4Å: Chain D: K.650, I.743, 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: 4 residues within 4Å: Chain D: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.130: 7 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.120 Ligand excluded by PLIP DMS.131: 4 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991 Ligand excluded by PLIP DMS.132: 5 residues within 4Å: Chain D: A.765, I.766, E.779, L.780, G.781 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: L.406, A.736, S.738, E.739 Ligand excluded by PLIP DMS.134: 4 residues within 4Å: Chain D: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.135: 6 residues within 4Å: Chain D: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.136: 6 residues within 4Å: Chain D: D.263, F.264, L.329, N.374, K.376, F.673 Ligand excluded by PLIP DMS.137: 5 residues within 4Å: Chain A: V.450 Chain D: R.311, G.312, G.313, A.315 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: P.936, L.939, C.968, G.969, Q.985 Ligand excluded by PLIP DMS.139: 5 residues within 4Å: Chain D: Y.501, T.523, T.525, D.526, R.560 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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