SMTL ID : 1jz3.1

E. COLI (lacZ) BETA-GALACTOSIDASE-TRAPPED 2-DEOXY-GALACTOSYL ENZYME INTERMEDIATE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

4 x 2DG: 2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

2DG.1: 12 residues within 4Å: Chain A: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.102, A:D.201, A:H.391 Water bridges: A:N.102, A:D.201, A:D.201, A:E.461 2DG.38: 11 residues within 4Å: Chain B: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604 Ligands: NA.42 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.102, B:D.201, B:H.391, B:N.460 Water bridges: B:N.102, B:D.201, B:D.201, B:D.201 2DG.74: 12 residues within 4Å: Chain C: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.80 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.102, C:H.391, C:N.460, C:Y.503 Water bridges: C:N.102, C:D.201, C:D.201, C:D.201 2DG.114: 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.119 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.391, D:N.460, D:Y.503 Water bridges: D:D.201, D:D.201, D:D.201

17 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: 7 residues within 4Å: Chain A: D.15, W.16, N.18, V.21, Y.161, 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: 3 residues within 4Å: Chain A: H.622, Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Ligands: DMS.16 No protein-ligand interaction detected (PLIP) MG.39: 4 residues within 4Å: Chain B: N.102, 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.44, H2O.46, H2O.49 MG.40: 5 residues within 4Å: Chain B: D.15, N.18, V.21, 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.41: 2 residues within 4Å: Chain B: Q.718 Ligands: DMS.68 No protein-ligand interaction detected (PLIP) MG.75: 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.86, H2O.88, H2O.91 MG.76: 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.77: 2 residues within 4Å: Chain C: Q.718 Ligands: DMS.107 No protein-ligand interaction detected (PLIP) MG.78: 1 residues within 4Å: Chain C: Q.49 No protein-ligand interaction detected (PLIP) MG.79: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.84: 2 residues within 4Å: Chain C: N.597, E.797 No protein-ligand interaction detected (PLIP) MG.115: 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.126, H2O.128, H2O.131 MG.116: 5 residues within 4Å: Chain D: D.15, N.18, V.21, 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 MG.117: 2 residues within 4Å: Chain D: Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.118: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.6: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: 2DG.1 Ligand excluded by PLIP NA.7: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.8: 4 residues within 4Å: Chain A: F.931, P.932, L.967, T.970 Ligand excluded by PLIP NA.9: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.31 Ligand excluded by PLIP NA.42: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 2DG.38 Ligand excluded by PLIP NA.43: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.44: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.45: 4 residues within 4Å: Chain B: S.647, E.650, L.670 Ligands: DMS.67 Ligand excluded by PLIP NA.80: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: 2DG.74 Ligand excluded by PLIP NA.81: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.82: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.83: 4 residues within 4Å: Chain C: S.647, E.650, L.670 Ligands: DMS.106 Ligand excluded by PLIP NA.119: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: 2DG.114 Ligand excluded by PLIP NA.120: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.121: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.122: 6 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.144 Ligand excluded by PLIP

4 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.10: 8 residues within 4Å: Chain A: N.102, V.103, H.418, E.461, F.601, W.999 Chain D: E.281 Ligands: DMS.36 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.102, A:N.102 Water bridges: A:D.201, A:E.461, A:W.999 pi-Cation interactions: A:W.999 BTB.46: 7 residues within 4Å: Chain B: N.102, V.103, H.418, E.461, W.999 Chain C: E.281 Ligands: DMS.71 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:N.102, B:N.102 Water bridges: B:D.201, B:E.461, B:W.999, C:E.281 BTB.85: 7 residues within 4Å: Chain B: E.281 Chain C: N.102, V.103, H.418, E.461, W.999 Ligands: DMS.111 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.102, C:N.102, C:E.461, C:E.461 Water bridges: C:W.999 BTB.123: 7 residues within 4Å: Chain A: E.281 Chain D: N.102, V.103, H.418, E.461, W.999 Ligands: DMS.147 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.102, D:N.102, D:E.461 Water bridges: D:W.999, D:W.999

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

DMS.11: 9 residues within 4Å: Chain A: V.227, T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.13: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.14: 7 residues within 4Å: Chain A: P.32, F.33, W.36, D.45, R.310, A.327 Ligands: DMS.32 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain A: T.271, L.291, R.292 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligands: MG.5 Ligand excluded by PLIP DMS.17: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.18: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain A: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain A: P.106, P.115, W.191 Ligands: DMS.23 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.22: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain A: G.593, D.594, T.595 Ligands: DMS.20 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.25: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain A: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: R.448, V.478 Ligand excluded by PLIP DMS.29: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain A: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.31: 7 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.9 Ligand excluded by PLIP DMS.32: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.14 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.34: 3 residues within 4Å: Chain A: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.35: 4 residues within 4Å: Chain A: S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain A: N.102, D.598, F.601, V.795 Ligands: BTB.10 Ligand excluded by PLIP DMS.37: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.47: 8 residues within 4Å: Chain B: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.48: 6 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.50: 6 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: E.314, H.316, G.320, T.321 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.54: 6 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: P.106, W.191 Ligands: DMS.59 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain B: G.593, D.594, T.595 Ligands: DMS.56 Ligand excluded by PLIP DMS.60: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain B: K.621, I.714, W.717 Ligand excluded by PLIP DMS.62: 2 residues within 4Å: Chain B: R.251, D.252 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.64: 2 residues within 4Å: Chain B: D.428 Chain C: V.478 Ligand excluded by PLIP DMS.65: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.66: 5 residues within 4Å: Chain B: Y.926, P.928, Y.962, R.973 Ligands: DMS.72 Ligand excluded by PLIP DMS.67: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.45 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: W.695, Q.719, W.720, R.721 Ligands: MG.41 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain B: E.57, W.58, L.125, T.126 Ligand excluded by PLIP DMS.70: 4 residues within 4Å: Chain B: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.71: 5 residues within 4Å: Chain B: N.102, D.598, F.601, V.795 Ligands: BTB.46 Ligand excluded by PLIP DMS.72: 6 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962, A.978 Ligands: DMS.66 Ligand excluded by PLIP DMS.73: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.86: 8 residues within 4Å: Chain C: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.87: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.88: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.89: 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.90: 4 residues within 4Å: Chain C: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.91: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.92: 4 residues within 4Å: Chain C: L.54, N.55, E.57, L.125 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.94: 4 residues within 4Å: Chain C: P.106, P.115, W.191 Ligands: DMS.102 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.96: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.97: 3 residues within 4Å: Chain C: G.593, D.594, T.595 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.99: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.100: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.101: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.102: 6 residues within 4Å: Chain C: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.94 Ligand excluded by PLIP DMS.103: 3 residues within 4Å: Chain B: W.474 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.104: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain C: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.106: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.83 Ligand excluded by PLIP DMS.107: 5 residues within 4Å: Chain C: W.695, Q.719, W.720, R.721 Ligands: MG.77 Ligand excluded by PLIP DMS.108: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.109: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.110: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.111: 5 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligands: BTB.85 Ligand excluded by PLIP DMS.112: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.113: 3 residues within 4Å: Chain C: Q.266, V.267, A.268 Ligand excluded by PLIP DMS.124: 8 residues within 4Å: Chain D: T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.126: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.127: 7 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.145 Ligand excluded by PLIP DMS.128: 4 residues within 4Å: Chain D: G.270, T.271, L.291, R.292 Ligand excluded by PLIP DMS.129: 4 residues within 4Å: Chain D: E.314, H.316, G.320 Ligands: DMS.149 Ligand excluded by PLIP DMS.130: 5 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.131: 4 residues within 4Å: Chain D: L.54, N.55, G.56, E.57 Ligand excluded by PLIP DMS.132: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: P.106, P.115, W.191 Ligands: DMS.136 Ligand excluded by PLIP DMS.134: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.135: 5 residues within 4Å: Chain D: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.136: 4 residues within 4Å: Chain D: G.593, D.594, T.595 Ligands: DMS.133 Ligand excluded by PLIP DMS.137: 3 residues within 4Å: Chain D: V.84, V.85, H.93 Ligand excluded by PLIP DMS.138: 3 residues within 4Å: Chain D: K.621, I.714, W.717 Ligand excluded by PLIP DMS.139: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.140: 6 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.141: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.142: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.143: 4 residues within 4Å: Chain D: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.144: 7 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.122 Ligand excluded by PLIP DMS.145: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.127 Ligand excluded by PLIP DMS.146: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.147: 5 residues within 4Å: Chain D: N.102, D.598, F.601, V.795 Ligands: BTB.123 Ligand excluded by PLIP DMS.148: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.149: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.129 Ligand excluded by PLIP DMS.150: 5 residues within 4Å: Chain D: Q.49, Q.50, D.130, S.132, W.133 Ligand excluded by PLIP DMS.151: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Juers, D.H. et al., A Structural View of the Action of Escherichia Coli (Lacz) Beta-Galactosidase. Biochemistry (2001)

Release Date

2001-12-07

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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