SMTL ID : 3mv0.1

E. COLI (lacZ) BETA-GALACTOSIDASE (R599A) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

149.1: 14 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 Ligands: NA.4, DMS.32 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.131, A:H.420, A:N.489, A:E.490 Water bridges: A:N.131, A:D.230, A:D.230, A:D.230 149.36: 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.40, DMS.70 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:D.230 149.76: 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.80, DMS.114 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:D.230, C:D.230 149.117: 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.121, DMS.151 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:H.420, D:N.489, D:E.490 Water bridges: D:N.131, D:D.230, D:D.230, D:D.230

11 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.37: 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.31, H2O.33, H2O.36 MG.38: 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.39: 2 residues within 4Å: Chain B: Q.747 Ligands: DMS.62 No protein-ligand interaction detected (PLIP) MG.77: 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.64, H2O.66, H2O.69 MG.78: 5 residues within 4Å: Chain C: D.44, 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.79: 2 residues within 4Å: Chain C: Q.747 Ligands: DMS.105 No protein-ligand interaction detected (PLIP) MG.118: 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.93, H2O.95, H2O.98 MG.119: 5 residues within 4Å: Chain D: D.44, 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 MG.120: 2 residues within 4Å: Chain D: Q.747, T.940 No protein-ligand interaction detected (PLIP)

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, E.679, L.699 Ligands: DMS.25 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: 149.36 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.42: 4 residues within 4Å: Chain B: F.960, P.961, L.996, T.999 Ligand excluded by PLIP NA.43: 6 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.61 Ligand excluded by PLIP NA.80: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: 149.76 Ligand excluded by PLIP NA.81: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.82: 4 residues within 4Å: Chain C: F.960, P.961, L.996, T.999 Ligand excluded by PLIP NA.83: 4 residues within 4Å: Chain C: S.676, E.679, L.699 Ligands: DMS.104 Ligand excluded by PLIP NA.121: 5 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 Ligands: 149.117 Ligand excluded by PLIP NA.122: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 Ligand excluded by PLIP NA.123: 4 residues within 4Å: Chain D: F.960, P.961, L.996, T.999 Ligand excluded by PLIP NA.124: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 Ligand excluded by PLIP

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

DMS.8: 8 residues within 4Å: Chain A: T.258, V.359, G.360, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: R.586, H.651, Q.652, 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.27 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain A: T.300, L.320, R.321 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: E.343, H.345, G.349, T.350, L.351 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: 4 residues within 4Å: Chain A: L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: P.135, P.144, W.220 Ligands: DMS.20, DMS.22 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain A: G.622, D.623, T.624 Ligands: DMS.17 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain A: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: Y.134, P.135, I.136, T.137 Ligands: DMS.17 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain A: D.457, P.459 Chain D: Q.474, R.477, V.507 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: S.676, D.677, N.678, E.679, N.733 Ligands: NA.7 Ligand excluded by PLIP DMS.26: 3 residues within 4Å: Chain A: W.724, Q.748, R.750 Ligand excluded by PLIP DMS.27: 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.28: 5 residues within 4Å: Chain A: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: R.66, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.32: 7 residues within 4Å: Chain A: N.131, V.132, H.447, E.490, S.825, W.1028 Ligands: 149.1 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain A: L.406, T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.34: 2 residues within 4Å: Chain A: E.96, A.97 Ligand excluded by PLIP DMS.35: 5 residues within 4Å: Chain A: R.311, G.312, G.313, A.315 Chain D: V.450 Ligand excluded by PLIP DMS.44: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.47: 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.48: 4 residues within 4Å: Chain B: T.300, L.320, R.321 Ligands: DMS.68 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain B: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain B: L.83, N.84, E.86, L.154 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain B: Y.134, P.135, I.136, T.137, P.625 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.54: 5 residues within 4Å: Chain B: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.55: 3 residues within 4Å: Chain B: V.113, V.114, H.122 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: K.650, I.743, W.746 Ligand excluded by PLIP DMS.57: 3 residues within 4Å: Chain B: L.279, R.280, D.281 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: F.260, N.261, D.262, E.363 Chain D: D.262 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: Y.955, Y.991, R.1002, H.1003 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain B: D.677, N.678, E.679 Ligands: NA.43 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain B: W.724, Q.748, W.749, R.750 Ligands: MG.39 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain B: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.64: 6 residues within 4Å: Chain B: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.65: 3 residues within 4Å: Chain B: S.952, R.990, Y.991 Ligand excluded by PLIP DMS.66: 4 residues within 4Å: Chain B: Y.501, T.523, T.525, D.526 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain B: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.68: 6 residues within 4Å: Chain B: A.297, S.298, R.321, L.322, N.323 Ligands: DMS.48 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain B: T.735, A.736, W.737, S.738, E.739 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain B: N.131, V.132, H.447, S.825, W.1028 Ligands: 149.36 Ligand excluded by PLIP DMS.71: 3 residues within 4Å: Chain B: R.433, Y.434, A.736 Ligand excluded by PLIP DMS.72: 4 residues within 4Å: Chain A: D.904 Chain B: R.750, L.751, A.752 Ligand excluded by PLIP DMS.73: 2 residues within 4Å: Chain B: D.316 Chain C: R.454 Ligand excluded by PLIP DMS.74: 6 residues within 4Å: Chain B: R.659, L.660, S.661, T.664, E.666, L.708 Ligand excluded by PLIP DMS.75: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: R.477, W.503, V.507 Ligand excluded by PLIP DMS.84: 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.85: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.86: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.87: 7 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.106 Ligand excluded by PLIP DMS.88: 3 residues within 4Å: Chain C: T.300, L.320, R.321 Ligand excluded by PLIP DMS.89: 5 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.90: 3 residues within 4Å: Chain C: L.83, N.84, L.154 Ligand excluded by PLIP DMS.91: 5 residues within 4Å: Chain C: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.92: 4 residues within 4Å: Chain C: P.135, P.144, W.220 Ligands: DMS.100 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain C: I.128, G.622, D.623, T.624 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: K.650, W.746 Ligands: DMS.111 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: F.260, N.261, D.262, E.363 Ligand excluded by PLIP DMS.100: 5 residues within 4Å: Chain C: Y.134, P.135, I.136, T.137 Ligands: DMS.92 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain B: V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.102: 3 residues within 4Å: Chain C: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.103: 3 residues within 4Å: Chain C: Y.955, Y.991, R.1002 Ligand excluded by PLIP DMS.104: 7 residues within 4Å: Chain C: S.676, D.677, N.678, E.679, P.732, N.733 Ligands: NA.83 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain C: W.724, Q.748, W.749, R.750 Ligands: MG.79 Ligand excluded by PLIP DMS.106: 7 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.87 Ligand excluded by PLIP DMS.107: 4 residues within 4Å: Chain C: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.108: 6 residues within 4Å: Chain C: R.66, Q.79, S.161, W.162, E.165, H.245 Ligand excluded by PLIP DMS.109: 4 residues within 4Å: Chain C: V.296, N.323, V.324, E.325 Ligand excluded by PLIP DMS.110: 3 residues within 4Å: Chain C: Q.295, V.296, A.297 Ligand excluded by PLIP DMS.111: 5 residues within 4Å: Chain C: T.726, I.743, W.746, C.943 Ligands: DMS.97 Ligand excluded by PLIP DMS.112: 7 residues within 4Å: Chain C: F.89, A.90, W.91, E.109, A.110, D.111, Y.124 Ligand excluded by PLIP DMS.113: 3 residues within 4Å: Chain C: I.334, P.335, N.336 Ligand excluded by PLIP DMS.114: 7 residues within 4Å: Chain C: N.131, V.132, H.447, F.630, S.825, W.1028 Ligands: 149.76 Ligand excluded by PLIP DMS.115: 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.116: 4 residues within 4Å: Chain C: R.750, L.751, A.752 Chain D: D.904 Ligand excluded by PLIP DMS.125: 9 residues within 4Å: Chain D: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.126: 6 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.127: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.128: 6 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, A.356 Ligand excluded by PLIP DMS.129: 3 residues within 4Å: Chain D: T.300, L.320, R.321 Ligand excluded by PLIP DMS.130: 4 residues within 4Å: Chain D: E.343, H.345, G.349 Ligands: DMS.148 Ligand excluded by PLIP DMS.131: 3 residues within 4Å: Chain D: E.537, V.1032, Q.1037 Ligand excluded by PLIP DMS.132: 5 residues within 4Å: Chain D: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.134: 4 residues within 4Å: Chain D: P.135, P.144, W.220 Ligands: DMS.137 Ligand excluded by PLIP DMS.135: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.136: 5 residues within 4Å: Chain D: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.137: 4 residues within 4Å: Chain D: G.622, D.623, T.624 Ligands: DMS.134 Ligand excluded by PLIP DMS.138: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.139: 3 residues within 4Å: Chain D: L.279, R.280, D.281 Ligand excluded by PLIP DMS.140: 6 residues within 4Å: Chain D: R.259, F.260, N.261, R.266, A.267, V.268 Ligand excluded by PLIP DMS.141: 4 residues within 4Å: Chain D: Y.134, P.135, I.136, T.137 Ligand excluded by PLIP DMS.142: 3 residues within 4Å: Chain D: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.143: 4 residues within 4Å: Chain D: Y.955, Y.991, R.1002 Ligands: DMS.147 Ligand excluded by PLIP DMS.144: 4 residues within 4Å: Chain D: W.724, Q.748, W.749, R.750 Ligand excluded by PLIP DMS.145: 6 residues within 4Å: Chain D: A.63, W.65, D.74, R.75, P.76, L.80 Ligand excluded by PLIP DMS.146: 3 residues within 4Å: Chain D: F.658, Q.747, W.749 Ligand excluded by PLIP DMS.147: 5 residues within 4Å: Chain D: S.952, Y.955, R.990, Y.991 Ligands: DMS.143 Ligand excluded by PLIP DMS.148: 2 residues within 4Å: Chain D: G.349 Ligands: DMS.130 Ligand excluded by PLIP DMS.149: 5 residues within 4Å: Chain D: Q.78, Q.79, D.159, S.161, W.162 Ligand excluded by PLIP DMS.150: 5 residues within 4Å: Chain D: W.162, L.163, Q.164, E.165, S.203 Ligand excluded by PLIP DMS.151: 7 residues within 4Å: Chain D: N.131, V.132, H.447, F.630, S.825, W.1028 Ligands: 149.117 Ligand excluded by PLIP DMS.152: 4 residues within 4Å: Chain D: P.817, V.836, Y.845, M.997 Ligand excluded by PLIP DMS.153: 2 residues within 4Å: Chain D: R.433, Y.434 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dugdale, M.L. et al., Importance of Arg-599 of b-galactosidase (Escherichia coli) as an anchor for the open conformations of Phe-601 and the active-site loop. Biochem.Cell Biol. (2010)

Release Date

2011-03-16

Peptides

Beta-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

Beta-galactosidase

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