SMTL ID : 3i3b.1

E.coli (lacz) Beta-Galactosidase (M542A) in Complex with D-Galactopyranosyl-1-on

Coordinates

PDB Format Compare

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.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.5, DMS.37 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.391, A:N.460, A:E.461 Water bridges: A:D.201, A:D.201, A:H.391 149.40: 14 residues within 4Å: Chain B: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.44 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:D.201, B:H.391, B:N.460, B:E.461 Water bridges: B:N.102, B:D.201, B:D.201, B:D.201 149.81: 14 residues within 4Å: Chain C: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.84 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:H.391, C:N.460, C:E.461 Water bridges: C:D.201, C:D.201, C:D.201 149.121: 12 residues within 4Å: Chain D: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.124 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.201, D:H.391, D:N.460, D:E.461 Water bridges: D:D.201, D:D.201, D:H.391

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

MG.2: 3 residues within 4Å: Chain A: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:H.418, A:E.461, H2O.1, H2O.3, H2O.6 MG.3: 5 residues within 4Å: Chain A: D.15, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193 MG.4: 2 residues within 4Å: Chain A: E.314 Ligands: DMS.14 No protein-ligand interaction detected (PLIP) MG.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 3 residues within 4Å: Chain B: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.416, B:H.418, B:E.461, H2O.32, H2O.34, H2O.37 MG.42: 6 residues within 4Å: Chain B: D.15, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193 MG.43: 3 residues within 4Å: Chain B: Q.718, T.911 Ligands: DMS.69 No protein-ligand interaction detected (PLIP) MG.82: 3 residues within 4Å: Chain C: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:H.418, C:E.461, H2O.63, H2O.69, H2O.92 MG.83: 5 residues within 4Å: Chain C: D.15, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193 MG.122: 3 residues within 4Å: Chain D: E.416, H.418, E.461 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:H.418, D:E.461, H2O.93, H2O.96, H2O.99 MG.123: 6 residues within 4Å: Chain D: D.15, N.18, V.21, Y.161, Q.163, D.193 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193

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

NA.5: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: 149.1 Ligand excluded by PLIP NA.6: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.25 Ligand excluded by PLIP NA.44: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 149.40 Ligand excluded by PLIP NA.45: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.46: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.47: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.68 Ligand excluded by PLIP NA.84: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: 149.81 Ligand excluded by PLIP NA.85: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.86: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.87: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.108 Ligand excluded by PLIP NA.124: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: 149.121 Ligand excluded by PLIP NA.125: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.126: 4 residues within 4Å: Chain D: F.931, P.932, L.967, T.970 Ligand excluded by PLIP NA.127: 5 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligand excluded by PLIP

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

DMS.9: 8 residues within 4Å: Chain A: T.229, V.330, G.331, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.10: 6 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.12: 7 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.27 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligands: MG.4 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: L.54, N.55, G.56, L.125 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: I.99, P.106, P.115 Ligands: DMS.22 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.20: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.18 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: D.428, P.430 Chain D: V.478 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, N.704 Ligands: NA.8 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: W.695, Q.718, Q.719, R.721 Ligand excluded by PLIP DMS.27: 6 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.12 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain A: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain A: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.32: 3 residues within 4Å: Chain A: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.33: 4 residues within 4Å: Chain A: R.37, N.38, S.39, L.322 Ligand excluded by PLIP DMS.34: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain A: E.57, R.59, L.125, T.126 Ligand excluded by PLIP DMS.36: 7 residues within 4Å: Chain A: L.377, Q.381, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.37: 7 residues within 4Å: Chain A: N.102, V.103, F.601, S.796, E.797, W.999 Ligands: 149.1 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain A: F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.39: 2 residues within 4Å: Chain A: L.822, L.823 Ligand excluded by PLIP DMS.48: 9 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.628, Q.718 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.51: 7 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: T.271, L.291, R.292 Ligands: DMS.75 Ligand excluded by PLIP DMS.53: 5 residues within 4Å: Chain B: S.39, E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain B: E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.55: 6 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.56: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.57: 6 residues within 4Å: Chain B: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.60 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.59: 5 residues within 4Å: Chain B: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.60: 2 residues within 4Å: Chain B: P.106 Ligands: DMS.57 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain B: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain B: K.621, I.714, W.717 Ligand excluded by PLIP DMS.63: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain B: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain B: D.428, P.430 Chain C: Q.445, R.448, V.478 Ligand excluded by PLIP DMS.66: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain B: Y.926, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: D.648, N.649, E.650, P.669 Ligands: NA.47 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain B: W.695, Q.719, W.720, R.721 Ligands: MG.43 Ligand excluded by PLIP DMS.70: 6 residues within 4Å: Chain B: E.57, W.58, R.59, S.124, L.125, T.126 Ligand excluded by PLIP DMS.71: 6 residues within 4Å: Chain B: R.37, Q.50, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.72: 6 residues within 4Å: Chain B: L.922, S.923, Y.926, R.961, Y.962, A.978 Ligand excluded by PLIP DMS.73: 4 residues within 4Å: Chain B: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.75: 6 residues within 4Å: Chain B: A.268, S.269, R.292, L.293, N.294 Ligands: DMS.52 Ligand excluded by PLIP DMS.76: 6 residues within 4Å: Chain B: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.77: 3 residues within 4Å: Chain B: I.305, P.306, N.307 Ligand excluded by PLIP DMS.78: 3 residues within 4Å: Chain B: R.404, Y.405, A.707 Ligand excluded by PLIP DMS.79: 6 residues within 4Å: Chain B: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.80: 6 residues within 4Å: Chain B: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.88: 8 residues within 4Å: Chain C: T.229, V.330, G.331, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.89: 6 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.91: 7 residues within 4Å: Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain C: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.96: 6 residues within 4Å: Chain C: I.99, P.106, P.115, W.191 Ligands: DMS.99, DMS.104 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.98: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.99: 3 residues within 4Å: Chain C: G.593, T.595 Ligands: DMS.96 Ligand excluded by PLIP DMS.100: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.102: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.103: 4 residues within 4Å: Chain C: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.104: 3 residues within 4Å: Chain C: Y.105, P.106 Ligands: DMS.96 Ligand excluded by PLIP DMS.105: 3 residues within 4Å: Chain B: V.478 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.106: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.107: 3 residues within 4Å: Chain C: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.108: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.87 Ligand excluded by PLIP DMS.109: 5 residues within 4Å: Chain C: W.695, Q.718, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.110: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.111: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.112: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.113: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.114: 3 residues within 4Å: Chain C: Q.266, V.267, A.268 Ligand excluded by PLIP DMS.115: 6 residues within 4Å: Chain C: F.60, A.61, W.62, E.80, A.81, D.82 Ligand excluded by PLIP DMS.116: 2 residues within 4Å: Chain B: D.287 Chain C: R.425 Ligand excluded by PLIP DMS.117: 3 residues within 4Å: Chain C: Y.253, T.317, D.319 Ligand excluded by PLIP DMS.118: 4 residues within 4Å: Chain C: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.119: 3 residues within 4Å: Chain C: I.305, P.306, N.307 Ligand excluded by PLIP DMS.120: 6 residues within 4Å: Chain C: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.128: 8 residues within 4Å: Chain D: T.229, V.330, G.331, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.129: 6 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.130: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.131: 7 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.149 Ligand excluded by PLIP DMS.132: 4 residues within 4Å: Chain D: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.133: 5 residues within 4Å: Chain D: E.314, H.316, G.320, L.322 Ligands: DMS.152 Ligand excluded by PLIP DMS.134: 3 residues within 4Å: Chain D: E.508, V.1003, Q.1008 Ligand excluded by PLIP DMS.135: 5 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.136: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.137: 5 residues within 4Å: Chain D: P.106, P.115, W.191 Ligands: DMS.140, DMS.145 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.139: 4 residues within 4Å: Chain D: G.275, G.276, T.290, R.292 Ligand excluded by PLIP DMS.140: 4 residues within 4Å: Chain D: G.593, D.594, T.595 Ligands: DMS.137 Ligand excluded by PLIP DMS.141: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.142: 3 residues within 4Å: Chain D: K.621, I.714, W.717 Ligand excluded by PLIP DMS.143: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.144: 5 residues within 4Å: Chain D: R.230, F.231, N.232, R.237, V.239 Ligand excluded by PLIP DMS.145: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108 Ligands: DMS.137 Ligand excluded by PLIP DMS.146: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.147: 3 residues within 4Å: Chain D: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.148: 4 residues within 4Å: Chain D: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.149: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.131 Ligand excluded by PLIP DMS.150: 3 residues within 4Å: Chain D: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.151: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.152: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.133 Ligand excluded by PLIP DMS.153: 4 residues within 4Å: Chain D: Q.49, Q.50, D.130, W.133 Ligand excluded by PLIP DMS.154: 5 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, S.174 Ligand excluded by PLIP DMS.155: 5 residues within 4Å: Chain D: A.736, I.737, H.739, L.751, G.752 Ligand excluded by PLIP DMS.156: 4 residues within 4Å: Chain D: V.807, K.811, Y.816, M.968 Ligand excluded by PLIP DMS.157: 4 residues within 4Å: Chain D: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dugdale, M.L. et al., Role of Met-542 as a guide for the conformational changes of Phe-601 that occur during the reaction of β-galactosidase (Escherichia coli). Biochem.Cell Biol. (2010)

Release Date

2010-05-12

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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