SMTL ID : 3dyo.1

E. coli (lacZ) beta-galactosidase (H418N) in complex with IPTG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.416, A:E.461, H2O.1, H2O.3, H2O.6 MG.2: 6 residues within 4Å: Chain A: D.15, N.18, P.19, V.21, 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.36: 3 residues within 4Å: Chain B: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.416, B:E.461, H2O.35, H2O.38, H2O.41 MG.37: 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.38: 1 residues within 4Å: Chain B: E.369 No protein-ligand interaction detected (PLIP) MG.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.74: 3 residues within 4Å: Chain C: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:E.461, H2O.73, H2O.76, H2O.79 MG.75: 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.76: 2 residues within 4Å: Chain C: Q.718 Ligands: DMS.103 No protein-ligand interaction detected (PLIP) MG.109: 3 residues within 4Å: Chain D: E.416, N.418, E.461 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:E.461, H2O.111, H2O.114, H2O.116 MG.110: 6 residues within 4Å: Chain D: D.15, N.18, P.19, 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 MG.111: 3 residues within 4Å: Chain D: H.622, Q.718, T.911 No protein-ligand interaction detected (PLIP)

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

NA.5: 6 residues within 4Å: Chain A: Y.100, D.201, W.568, F.601, N.604 Ligands: IPT.9 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: 1 residues within 4Å: Chain A: N.597 Ligand excluded by PLIP NA.40: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: IPT.46 Ligand excluded by PLIP NA.41: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.42: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.43: 4 residues within 4Å: Chain B: S.647, E.650, L.670 Ligands: DMS.67 Ligand excluded by PLIP NA.44: 2 residues within 4Å: Chain B: N.597, E.797 Ligand excluded by PLIP NA.77: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: IPT.83 Ligand excluded by PLIP NA.78: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.79: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.80: 4 residues within 4Å: Chain C: S.647, E.650, L.670 Ligands: DMS.102 Ligand excluded by PLIP NA.81: 2 residues within 4Å: Chain C: N.597, E.797 Ligand excluded by PLIP NA.112: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: IPT.117 Ligand excluded by PLIP NA.113: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.114: 4 residues within 4Å: Chain D: F.931, P.932, L.967, T.970 Ligand excluded by PLIP NA.115: 1 residues within 4Å: Chain D: N.597 Ligand excluded by PLIP

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

IPT.9: 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.5 9 PLIP interactions: 9 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:N.460, A:E.461, A:E.461 IPT.10: 11 residues within 4Å: Chain A: E.304, I.305, P.306, Y.642, R.645, D.648, E.650, Q.702, T.706, W.708 Ligands: DMS.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.708 Hydrogen bonds: A:R.645, A:D.648, A:W.708 Water bridges: A:H.646, A:W.708 IPT.35: 7 residues within 4Å: Chain A: R.230, F.231, N.232, R.237, A.238, V.239 Chain C: D.233 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:R.237, A:V.239 Hydrogen bonds: A:R.230, A:R.230, C:D.233 Water bridges: A:D.233, C:D.233, C:D.234 IPT.45: 5 residues within 4Å: Chain A: D.507, E.508 Chain B: K.521, Q.554, Q.558 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.558, B:Q.558 Water bridges: B:D.507, B:K.521, B:K.521, A:D.507, A:D.509, A:K.521 Hydrophobic interactions: A:E.508 IPT.46: 13 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.40, DMS.72 8 PLIP interactions: 8 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:N.418, B:E.461 IPT.73: 8 residues within 4Å: Chain B: R.230, F.231, N.232, R.237, A.238, V.239 Chain D: D.233, D.234 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:R.237, B:V.239 Hydrogen bonds: B:R.230, B:R.230, D:D.233 Water bridges: B:N.232 IPT.82: 7 residues within 4Å: Chain A: D.233 Chain C: R.230, F.231, N.232, R.237, A.238, V.239 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.230, C:R.230, A:D.233 Water bridges: C:N.232, C:D.233 IPT.83: 12 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.77 8 PLIP interactions: 8 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:N.460, C:E.461 IPT.108: 4 residues within 4Å: Chain C: Q.554, Q.558 Chain D: D.507, E.508 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:Q.554, C:Q.558, C:Q.558, D:D.507 Water bridges: C:K.521, D:D.507, D:K.521 Hydrophobic interactions: D:E.508 IPT.116: 7 residues within 4Å: Chain B: D.233 Chain D: R.230, F.231, N.232, R.237, A.238, V.239 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:D.233, D:R.230, D:R.230 Water bridges: B:D.233, B:D.234 Hydrophobic interactions: D:R.237, D:V.239 IPT.117: 12 residues within 4Å: Chain D: N.102, D.201, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.112 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:W.999 Hydrogen bonds: D:N.102, D:E.461, D:Y.503, D:F.601, D:N.604 Water bridges: D:D.201, D:H.391, D:N.460, D:E.461, D:E.461, D:E.461, D:E.461 IPT.118: 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.121 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.645, D:D.648, D:W.708 Water bridges: D:A.707, D:W.708

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

DMS.11: 8 residues within 4Å: Chain A: 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: 7 residues within 4Å: Chain A: K.380, N.383, F.626, Y.642, Q.702, W.708 Ligands: IPT.10 Ligand excluded by PLIP DMS.14: 8 residues within 4Å: Chain A: P.32, F.33, A.34, 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: 4 residues within 4Å: Chain A: E.314, H.316, G.320, L.322 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: 5 residues within 4Å: Chain A: L.54, N.55, W.58, L.125, F.127 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: E.334, V.335, P.480, S.481 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain A: I.99, P.106, P.115, W.191 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: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.24: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.25: 3 residues within 4Å: Chain A: K.621, I.714, W.717 Ligand excluded by PLIP DMS.26: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain A: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: R.448, V.478 Ligand excluded by PLIP DMS.30: 4 residues within 4Å: Chain A: D.82, H.93, G.94, Y.95 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain A: Y.926, Y.962, R.973, L.976 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: 5 residues within 4Å: Chain A: R.37, Q.50, S.132, W.133, H.216 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: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, Q.702, W.708 Ligand excluded by PLIP DMS.50: 8 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.69 Ligand excluded by PLIP DMS.51: 3 residues within 4Å: Chain B: T.271, L.291, R.292 Ligand excluded by PLIP DMS.52: 4 residues within 4Å: Chain B: T.257, E.314, H.316, G.320 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: 5 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: P.106, P.115, W.191 Ligand excluded by PLIP DMS.57: 4 residues within 4Å: Chain B: P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.58: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain B: G.593, D.594, T.595 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain B: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.61: 2 residues within 4Å: Chain B: K.621, W.717 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.63: 6 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain B: D.428 Chain C: Q.445, W.474, 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: 4 residues within 4Å: Chain B: Y.926, P.928, Y.962, R.973 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.43 Ligand excluded by PLIP DMS.68: 2 residues within 4Å: Chain B: Q.719, R.721 Ligand excluded by PLIP DMS.69: 6 residues within 4Å: Chain B: W.36, D.45, R.46, P.47, S.48 Ligands: DMS.50 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: 5 residues within 4Å: Chain B: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain B: N.102, D.598, F.601, V.795 Ligands: IPT.46 Ligand excluded by PLIP DMS.84: 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.85: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.86: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.87: 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.88: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.89: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain C: S.53, L.54, N.55, E.57, L.125 Ligand excluded by PLIP DMS.91: 4 residues within 4Å: Chain C: E.334, V.335, P.480, S.481 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain C: P.106, P.115, W.191 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.94: 6 residues within 4Å: Chain C: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.95: 3 residues within 4Å: Chain C: G.593, D.594, T.595 Ligand excluded by PLIP DMS.96: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.97: 2 residues within 4Å: Chain C: K.621, W.717 Ligand excluded by PLIP DMS.98: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.99: 3 residues within 4Å: Chain B: V.478 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain C: D.82, H.93, G.94, Y.95 Ligand excluded by PLIP DMS.101: 3 residues within 4Å: Chain C: Y.926, Y.962, R.973 Ligand excluded by PLIP DMS.102: 7 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.80 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain C: W.695, Q.719, W.720, R.721 Ligands: MG.76 Ligand excluded by PLIP DMS.104: 5 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain C: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.106: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.107: 5 residues within 4Å: Chain C: R.37, Q.50, S.132, W.133, H.216 Ligand excluded by PLIP DMS.119: 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.120: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.121: 7 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, Q.702, W.708 Ligands: IPT.118 Ligand excluded by PLIP DMS.122: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.139 Ligand excluded by PLIP DMS.123: 4 residues within 4Å: Chain D: G.270, T.271, L.291, R.292 Ligand excluded by PLIP DMS.124: 3 residues within 4Å: Chain D: E.314, H.316, G.320 Ligand excluded by PLIP DMS.125: 4 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.126: 6 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, W.58, L.125 Ligand excluded by PLIP DMS.127: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.128: 3 residues within 4Å: Chain D: P.106, P.115, W.191 Ligand excluded by PLIP DMS.129: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.130: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.131: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.132: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.133: 4 residues within 4Å: Chain D: K.621, R.699, I.714, W.717 Ligand excluded by PLIP DMS.134: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.135: 5 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.136: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.137: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.138: 5 residues within 4Å: Chain D: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.139: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.122 Ligand excluded by PLIP DMS.140: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.141: 5 residues within 4Å: Chain D: 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., Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli). Protein Sci. (2009)

Release Date

2008-10-28

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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