SMTL ID : 3i3e.1

E. COLI (lacZ) BETA-GALACTOSIDASE (M542A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 4 residues within 4Å: Chain A: N.102, 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: 6 residues within 4Å: Chain A: D.15, N.18, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.15, A:N.18, A:V.21, A:D.193, A:D.193 MG.3: 1 residues within 4Å: Chain A: Q.718 No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.42: 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.37, H2O.40, H2O.43 MG.43: 6 residues within 4Å: Chain B: D.15, N.18, V.21, Y.161, 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.44: 2 residues within 4Å: Chain B: Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.84: 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.73, H2O.76, H2O.79 MG.85: 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.86: 2 residues within 4Å: Chain C: Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.87: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.124: 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.125: 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 MG.126: 2 residues within 4Å: Chain D: Q.718, T.911 No protein-ligand interaction detected (PLIP)

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

NA.5: 4 residues within 4Å: Chain A: D.201, H.540, F.601, N.604 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.26 Ligand excluded by PLIP NA.45: 4 residues within 4Å: Chain B: D.201, H.540, F.601, N.604 Ligand excluded by PLIP NA.46: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.47: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.48: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.68 Ligand excluded by PLIP NA.88: 4 residues within 4Å: Chain C: D.201, H.540, F.601, N.604 Ligand excluded by PLIP NA.89: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.90: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.91: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.112 Ligand excluded by PLIP NA.127: 4 residues within 4Å: Chain D: D.201, H.540, F.601, N.604 Ligand excluded by PLIP NA.128: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.129: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.130: 6 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.150 Ligand excluded by PLIP

133 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: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 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.28 Ligand excluded by PLIP DMS.13: 3 residues within 4Å: Chain A: T.271, L.291, R.292 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.16: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 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: P.106, P.115, W.191 Ligands: DMS.23 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: G.593, D.594, T.595 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108 Ligands: DMS.18 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: R.448, V.478 Ligand excluded by PLIP DMS.25: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, N.704 Ligands: NA.8 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain A: W.695, Q.719, R.721 Ligand excluded by PLIP DMS.28: 7 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.12 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain A: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.31: 5 residues within 4Å: Chain A: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.33: 3 residues within 4Å: Chain A: R.699, I.714, W.717 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain A: R.282, G.283, G.284 Chain D: V.421 Ligand excluded by PLIP DMS.35: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.36: 1 residues within 4Å: Chain A: P.306 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain A: Y.472, T.493, T.494, T.496, R.531 Ligand excluded by PLIP DMS.38: 4 residues within 4Å: Chain A: R.630, S.632, T.635, E.637 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain A: R.230, F.231, N.232, R.237, V.239 Ligand excluded by PLIP DMS.40: 1 residues within 4Å: Chain A: T.741 Ligand excluded by PLIP DMS.49: 8 residues within 4Å: Chain B: T.229, V.330, G.331, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.52: 6 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain B: T.271, L.291, R.292 Ligand excluded by PLIP DMS.54: 4 residues within 4Å: Chain B: E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.57: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.58: 5 residues within 4Å: Chain B: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.59: 6 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligands: DMS.81 Ligand excluded by PLIP DMS.60: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.61: 3 residues within 4Å: Chain B: P.106, P.115, W.191 Ligand excluded by PLIP DMS.62: 4 residues within 4Å: Chain B: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.63: 3 residues within 4Å: Chain B: K.621, I.714, W.717 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 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 Ligands: DMS.72 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain B: D.648, N.649, E.650, N.704 Ligands: NA.48 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain B: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.70: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain B: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.72: 6 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962, A.978 Ligands: DMS.67 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.74: 6 residues within 4Å: Chain B: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.75: 6 residues within 4Å: Chain B: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.76: 4 residues within 4Å: Chain B: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.77: 4 residues within 4Å: Chain B: S.269, R.292, L.293, N.294 Ligand excluded by PLIP DMS.78: 2 residues within 4Å: Chain B: R.404, Y.405 Ligand excluded by PLIP DMS.79: 6 residues within 4Å: Chain B: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.80: 4 residues within 4Å: Chain B: L.341, L.343, G.346, P.348 Ligand excluded by PLIP DMS.81: 5 residues within 4Å: Chain B: F.608, D.610, T.612, R.973 Ligands: DMS.59 Ligand excluded by PLIP DMS.82: 5 residues within 4Å: Chain B: R.630, S.632, T.635, E.637, L.679 Ligand excluded by PLIP DMS.83: 2 residues within 4Å: Chain B: D.428 Chain C: V.478 Ligand excluded by PLIP DMS.92: 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.93: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.95: 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.96: 4 residues within 4Å: Chain C: T.271, L.291, R.292 Ligands: DMS.120 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain C: R.505, E.508, P.1001, S.1002, V.1003 Ligand excluded by PLIP DMS.98: 5 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain C: P.106, P.115, W.191 Ligands: DMS.108 Ligand excluded by PLIP DMS.101: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.102: 6 residues within 4Å: Chain C: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.103: 2 residues within 4Å: Chain C: G.593, T.595 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain C: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.105: 2 residues within 4Å: Chain C: K.621, W.717 Ligand excluded by PLIP DMS.106: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.107: 4 residues within 4Å: Chain C: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.108: 5 residues within 4Å: Chain C: Y.105, P.106, I.107, T.108 Ligands: DMS.100 Ligand excluded by PLIP DMS.109: 3 residues within 4Å: Chain B: W.474 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.110: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.111: 4 residues within 4Å: Chain C: Y.926, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.112: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.91 Ligand excluded by PLIP DMS.113: 2 residues within 4Å: Chain C: Q.719, R.721 Ligand excluded by PLIP DMS.114: 5 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.115: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.117: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.118: 4 residues within 4Å: Chain C: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain C: Q.381, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.120: 6 residues within 4Å: Chain C: A.268, S.269, R.292, L.293, N.294 Ligands: DMS.96 Ligand excluded by PLIP DMS.121: 3 residues within 4Å: Chain C: I.305, P.306, N.307 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain C: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.123: 6 residues within 4Å: Chain C: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.131: 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.132: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.133: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.134: 6 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.135: 4 residues within 4Å: Chain D: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.136: 5 residues within 4Å: Chain D: E.314, H.316, G.320, T.321 Ligands: DMS.155 Ligand excluded by PLIP DMS.137: 4 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.139: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.140: 3 residues within 4Å: Chain D: P.106, P.115 Ligands: DMS.147 Ligand excluded by PLIP DMS.141: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.142: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.143: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.144: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.145: 2 residues within 4Å: Chain D: K.621, W.717 Ligand excluded by PLIP DMS.146: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.147: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108 Ligands: DMS.140 Ligand excluded by PLIP DMS.148: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.149: 3 residues within 4Å: Chain D: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.150: 6 residues within 4Å: Chain D: D.648, N.649, E.650, P.703, N.704 Ligands: NA.130 Ligand excluded by PLIP DMS.151: 4 residues within 4Å: Chain D: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.152: 5 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.153: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.154: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.155: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.136 Ligand excluded by PLIP DMS.156: 4 residues within 4Å: Chain D: Q.49, Q.50, D.130, W.133 Ligand excluded by PLIP DMS.157: 5 residues within 4Å: Chain A: H.226, W.474, V.478 Chain D: D.428, P.430 Ligand excluded by PLIP DMS.158: 4 residues within 4Å: Chain C: R.721, L.722, A.723 Chain D: D.875 Ligand excluded by PLIP DMS.159: 6 residues within 4Å: Chain D: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.160: 4 residues within 4Å: Chain D: R.630, S.632, T.635, E.637 Ligand excluded by PLIP DMS.161: 5 residues within 4Å: Chain D: I.737, H.739, E.750, L.751, G.752 Ligand excluded by PLIP DMS.162: 1 residues within 4Å: Chain D: Y.405 Ligand excluded by PLIP DMS.163: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP DMS.164: 6 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334, R.336 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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