SMTL ID : 3muy.1

E. coli (lacZ) beta-galactosidase (R599A)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

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

DMS.1: 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.2: 5 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.3: 5 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.4: 8 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.17 Ligand excluded by PLIP DMS.5: 3 residues within 4Å: Chain A: T.271, L.291, R.292 Ligand excluded by PLIP DMS.6: 6 residues within 4Å: Chain A: E.314, H.316, G.320, T.321, L.322 Ligands: MG.23 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.8: 3 residues within 4Å: Chain A: L.54, N.55, L.125 Ligand excluded by PLIP DMS.9: 4 residues within 4Å: Chain A: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.11: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.13: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.14: 1 residues within 4Å: Chain A: P.596 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.16: 7 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.26 Ligand excluded by PLIP DMS.17: 6 residues within 4Å: Chain A: A.34, W.36, R.46, P.47, L.51 Ligands: DMS.4 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.27: 2 residues within 4Å: Chain A: R.404, Y.405 Ligand excluded by PLIP DMS.28: 3 residues within 4Å: Chain A: E.744, R.760, Q.761 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: G.248, E.249, L.250, R.251 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain A: N.38, S.39, E.314, L.322 Ligand excluded by PLIP DMS.31: 3 residues within 4Å: Chain A: Y.472, T.494, T.496 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.33: 4 residues within 4Å: Chain A: S.963, Q.966, E.969, E.979 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: 8 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.66 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain B: G.270, T.271, L.291, R.292, L.293 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.40: 6 residues within 4Å: Chain B: S.53, L.54, N.55, G.56, W.58, L.125 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.42: 3 residues within 4Å: Chain B: I.99, P.106 Ligands: DMS.65 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain B: G.275, V.289, T.290, R.292 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: F.231, N.232, D.233, E.334, R.336 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: D.428 Chain C: H.226, R.448, V.478 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: Y.926, Y.962, R.973, H.974, L.976 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: D.648, N.649, E.650, N.704 Ligands: NA.59 Ligand excluded by PLIP DMS.52: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.53: 6 residues within 4Å: Chain B: R.37, Q.50, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: S.923, Y.926, Y.962 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.62: 6 residues within 4Å: Chain B: R.230, F.231, N.232, R.237, A.238, V.239 Ligand excluded by PLIP DMS.63: 4 residues within 4Å: Chain B: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.64: 3 residues within 4Å: Chain B: R.404, Y.405, A.707 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain B: Y.105, P.106, I.107, P.596 Ligands: DMS.42 Ligand excluded by PLIP DMS.66: 7 residues within 4Å: Chain B: A.34, W.36, D.45, R.46, P.47, S.48 Ligands: DMS.37 Ligand excluded by PLIP DMS.67: 2 residues within 4Å: Chain B: P.306, N.307 Ligand excluded by PLIP DMS.68: 3 residues within 4Å: Chain B: L.250, D.287 Chain C: R.425 Ligand excluded by PLIP DMS.69: 6 residues within 4Å: Chain B: S.963, Q.965, Q.966, E.969, H.977, E.979 Ligand excluded by PLIP DMS.70: 4 residues within 4Å: Chain B: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.71: 5 residues within 4Å: Chain B: Q.783, F.784, T.785, H.815, W.842 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain B: F.989, A.1011, R.1013, Y.1014, H.1015 Ligand excluded by PLIP DMS.73: 1 residues within 4Å: Chain B: Q.266 Ligand excluded by PLIP DMS.74: 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.75: 4 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.628 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.77: 8 residues within 4Å: Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.94 Ligand excluded by PLIP DMS.78: 6 residues within 4Å: Chain C: G.270, T.271, L.291, R.292, L.293 Ligands: DMS.112 Ligand excluded by PLIP DMS.79: 5 residues within 4Å: Chain C: R.505, E.508, P.1001, S.1002, V.1003 Ligand excluded by PLIP DMS.80: 4 residues within 4Å: Chain C: S.53, L.54, N.55, L.125 Ligand excluded by PLIP DMS.81: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.82: 2 residues within 4Å: Chain C: P.106 Ligands: DMS.106 Ligand excluded by PLIP DMS.83: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.84: 4 residues within 4Å: Chain C: G.275, V.289, T.290, R.292 Ligand excluded by PLIP DMS.85: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.86: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.87: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.88: 4 residues within 4Å: Chain C: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.89: 2 residues within 4Å: Chain B: V.478 Chain C: D.428 Ligand excluded by PLIP DMS.90: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.91: 4 residues within 4Å: Chain C: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.92: 6 residues within 4Å: Chain C: D.648, N.649, E.650, P.703, N.704 Ligands: NA.101 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain C: N.102, W.999 Ligands: DMS.103 Ligand excluded by PLIP DMS.94: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.77 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligands: DMS.93 Ligand excluded by PLIP DMS.104: 4 residues within 4Å: Chain C: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain C: A.61, W.62, E.80, D.82, Y.95 Ligand excluded by PLIP DMS.106: 6 residues within 4Å: Chain C: T.104, Y.105, P.106, T.108, P.596 Ligands: DMS.82 Ligand excluded by PLIP DMS.107: 4 residues within 4Å: Chain C: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.108: 3 residues within 4Å: Chain C: W.695, Q.719, W.720 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: 3 residues within 4Å: Chain C: R.404, Y.405, A.707 Ligand excluded by PLIP DMS.111: 3 residues within 4Å: Chain C: W.918, D.919, L.920 Ligand excluded by PLIP DMS.112: 6 residues within 4Å: Chain C: A.268, S.269, R.292, L.293, N.294 Ligands: DMS.78 Ligand excluded by PLIP DMS.113: 3 residues within 4Å: Chain C: I.305, P.306, N.307 Ligand excluded by PLIP DMS.114: 2 residues within 4Å: Chain C: G.771, D.772 Ligand excluded by PLIP DMS.115: 3 residues within 4Å: Chain C: R.721, L.722 Chain D: D.875 Ligand excluded by PLIP DMS.116: 3 residues within 4Å: Chain A: E.797 Chain D: E.281, R.282 Ligand excluded by PLIP DMS.117: 9 residues within 4Å: Chain D: T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.118: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.120: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.134 Ligand excluded by PLIP DMS.121: 4 residues within 4Å: Chain D: G.270, T.271, L.291, R.292 Ligand excluded by PLIP DMS.122: 5 residues within 4Å: Chain D: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.123: 6 residues within 4Å: Chain D: S.53, L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.124: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.125: 3 residues within 4Å: Chain D: P.106, I.107 Ligands: DMS.131 Ligand excluded by PLIP DMS.126: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.127: 4 residues within 4Å: Chain D: G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.128: 3 residues within 4Å: Chain D: V.84, V.85, H.93 Ligand excluded by PLIP DMS.129: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.130: 5 residues within 4Å: Chain D: F.231, N.232, D.233, E.334, R.336 Ligand excluded by PLIP DMS.131: 6 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.125 Ligand excluded by PLIP DMS.132: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.134: 6 residues within 4Å: Chain D: A.34, D.45, R.46, P.47, L.51 Ligands: DMS.120 Ligand excluded by PLIP DMS.135: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.136: 2 residues within 4Å: Chain D: S.923, Y.962 Ligand excluded by PLIP DMS.137: 3 residues within 4Å: Chain D: G.320, T.321, L.322 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: Q.49, Q.50, D.130, S.132, W.133 Ligand excluded by PLIP DMS.139: 6 residues within 4Å: Chain D: W.133, L.134, Q.135, E.136, G.137, S.174 Ligand excluded by PLIP DMS.145: 2 residues within 4Å: Chain D: R.404, Y.405 Ligand excluded by PLIP DMS.146: 7 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.147 Ligand excluded by PLIP DMS.149: 6 residues within 4Å: Chain D: D.782, Q.783, F.784, T.785, H.815, W.842 Ligand excluded by PLIP DMS.150: 5 residues within 4Å: Chain A: H.226, R.448, V.478 Chain D: D.428, P.430 Ligand excluded by PLIP DMS.151: 5 residues within 4Å: Chain D: R.230, F.231, N.232, R.237, V.239 Ligand excluded by PLIP DMS.152: 4 residues within 4Å: Chain D: D.45, R.310, D.329, R.404 Ligand excluded by PLIP DMS.153: 2 residues within 4Å: Chain D: L.910, Q.956 Ligand excluded by PLIP DMS.154: 4 residues within 4Å: Chain D: Y.472, T.494, T.496, R.531 Ligand excluded by PLIP DMS.155: 1 residues within 4Å: Chain D: H.646 Ligand excluded by PLIP DMS.156: 4 residues within 4Å: Chain D: E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP

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

MG.21: 3 residues within 4Å: Chain A: E.416, H.418, E.461 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.418, A:E.461, H2O.1, H2O.3, H2O.6 MG.22: 6 residues within 4Å: Chain A: D.15, 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.23: 1 residues within 4Å: Ligands: DMS.6 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain B: E.416, H.418, E.461 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.418, B:E.461, H2O.34, H2O.36, H2O.39 MG.57: 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.96: 3 residues within 4Å: Chain C: E.416, H.418, E.461 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.418, C:E.461, H2O.65, H2O.68, H2O.70 MG.97: 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.140: 3 residues within 4Å: Chain D: E.416, H.418, E.461 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.418, D:E.461, H2O.97, H2O.100, H2O.103 MG.141: 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.148: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.24: 4 residues within 4Å: Chain A: D.201, W.568, F.601, N.604 Ligand excluded by PLIP NA.25: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.26: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.16 Ligand excluded by PLIP NA.58: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.59: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.51 Ligand excluded by PLIP NA.60: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.61: 4 residues within 4Å: Chain B: D.201, H.540, F.601, N.604 Ligand excluded by PLIP NA.98: 3 residues within 4Å: Chain C: D.201, F.601, N.604 Ligand excluded by PLIP NA.99: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.100: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.101: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.92 Ligand excluded by PLIP NA.102: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP NA.142: 4 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligand excluded by PLIP NA.143: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.144: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.147: 4 residues within 4Å: Chain D: S.647, E.650, L.670 Ligands: DMS.146 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dugdale, M.L. et al., Importance of Arg-599 of beta-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-D-galactosidase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
1

B
2

C
3

D
4

Beta-D-galactosidase