SMTL ID : 1jyx.1

E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH IPTG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

9 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.2: 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.26: 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.35, H2O.37, H2O.40 MG.27: 5 residues within 4Å: Chain B: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193, B:D.193 MG.28: 1 residues within 4Å: Chain B: E.369 No protein-ligand interaction detected (PLIP) MG.52: 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.71, H2O.73, H2O.76 MG.53: 7 residues within 4Å: Chain C: D.15, W.16, N.18, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193, C:D.193 MG.80: 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.107, H2O.109, H2O.112 MG.81: 5 residues within 4Å: Chain D: D.15, N.18, V.21, Q.163, D.193 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.15, D:N.18, D:V.21, D:D.193, D:D.193

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

NA.3: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: IPT.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.201, A:N.604 NA.4: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.556, A:L.562 NA.5: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.967 NA.29: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: IPT.33 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.201, B:N.604 NA.30: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.556, B:L.562 NA.31: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.932 NA.32: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.49 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.647, B:E.650, B:L.670 NA.54: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: IPT.58 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.100, C:Y.100, C:N.604 NA.55: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.556, C:L.562 NA.56: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.968 NA.57: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.76 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.650, C:E.650, C:L.670 NA.82: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: IPT.85 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.100, D:D.201, D:N.604 NA.83: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.560, D:L.562 NA.84: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:T.970

6 x IPT: 1-methylethyl 1-thio-beta-D-galactopyranoside(Non-covalent)

IPT.6: 12 residues within 4Å: Chain A: N.102, D.201, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.999 Hydrogen bonds: A:N.102, A:D.201, A:E.461, A:F.601, A:N.604 Water bridges: A:D.201, A:H.418, A:E.461, A:E.461, A:E.461, A:E.537 IPT.7: 10 residues within 4Å: Chain A: E.304, P.306, Y.642, R.645, D.648, E.650, Q.702, T.706, W.708 Ligands: DMS.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.645, A:D.648, A:W.708 Water bridges: A:W.708 IPT.33: 12 residues within 4Å: Chain B: N.102, D.201, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.29 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.999 Hydrogen bonds: B:N.102, B:D.201, B:E.461, B:F.601, B:N.604 Water bridges: B:H.418, B:N.460, B:E.461 IPT.58: 13 residues within 4Å: Chain C: N.102, D.201, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.54, DMS.79 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:W.999 Hydrogen bonds: C:N.102, C:E.461, C:Y.503, C:F.601, C:N.604 Water bridges: C:H.418, C:N.460, C:E.461 IPT.85: 13 residues within 4Å: Chain D: N.102, D.201, H.418, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.82 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:W.999, D:W.999 Hydrogen bonds: D:N.102, D:D.201, D:E.461, D:Y.503, D:F.601, D:N.604 Water bridges: D:H.418, D:N.460, D:E.461 IPT.86: 10 residues within 4Å: Chain D: E.304, P.306, Y.642, R.645, D.648, E.650, Q.702, T.706, W.708 Ligands: DMS.89 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.708 Hydrogen bonds: D:R.645, D:D.648, D:W.708 Water bridges: D:A.707, D:W.708

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

DMS.8: 9 residues within 4Å: Chain A: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.10: 7 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, Q.702, W.708 Ligands: IPT.7 Ligand excluded by PLIP DMS.11: 8 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.23 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain A: T.271, L.291, R.292 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain A: P.106, P.115, W.191 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.18: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: K.621, I.714, W.717 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: D.428, P.430 Chain D: V.478 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.23: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.11 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.25: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.34: 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.35: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.36: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.37: 7 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligands: DMS.50 Ligand excluded by PLIP DMS.38: 3 residues within 4Å: Chain B: T.271, L.291, R.292 Ligand excluded by PLIP DMS.39: 3 residues within 4Å: Chain B: E.314, H.316, G.320 Ligand excluded by PLIP DMS.40: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain B: S.53, L.54, N.55, E.57, L.125, F.127 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.43: 3 residues within 4Å: Chain B: P.106, P.115, W.191 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain B: G.593, D.594, T.595 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain B: D.428 Chain C: W.474, V.478 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.49: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.32 Ligand excluded by PLIP DMS.50: 6 residues within 4Å: Chain B: W.36, D.45, R.46, P.47, S.48 Ligands: DMS.37 Ligand excluded by PLIP DMS.51: 4 residues within 4Å: Chain B: E.57, W.58, L.125, T.126 Ligand excluded by PLIP DMS.59: 9 residues within 4Å: Chain C: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.60: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.61: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.62: 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.63: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain C: E.314, H.316, G.320, T.321 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.66: 6 residues within 4Å: Chain C: S.53, L.54, N.55, E.57, L.125, F.127 Ligand excluded by PLIP DMS.67: 5 residues within 4Å: Chain C: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.68: 4 residues within 4Å: Chain C: I.99, P.106, P.115, W.191 Ligand excluded by PLIP DMS.69: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.70: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain C: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.72: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.73: 1 residues within 4Å: Chain C: D.428 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain C: D.82, H.93, G.94, Y.95 Ligand excluded by PLIP DMS.75: 6 residues within 4Å: Chain C: S.796, E.797, A.798, I.801, E.808, K.811 Ligand excluded by PLIP DMS.76: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, N.704 Ligands: NA.57 Ligand excluded by PLIP DMS.77: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.78: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.79: 5 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligands: IPT.58 Ligand excluded by PLIP DMS.87: 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.88: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.89: 6 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligands: IPT.86 Ligand excluded by PLIP DMS.90: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.102 Ligand excluded by PLIP DMS.91: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.92: 4 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.93: 4 residues within 4Å: Chain D: L.54, N.55, E.57, L.125 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain D: I.99, P.106, I.107, P.115, W.191 Ligand excluded by PLIP DMS.96: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain D: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.99: 3 residues within 4Å: Chain D: V.84, V.85, H.93 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain D: K.621, R.699, I.714, W.717 Ligand excluded by PLIP DMS.101: 5 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.102: 7 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.90 Ligand excluded by PLIP DMS.103: 4 residues within 4Å: Chain A: R.282, G.284, A.286 Chain D: V.421 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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