SMTL ID : 1jz4.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

2DG.1: 11 residues within 4Å: Chain A: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604 Ligands: NA.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.201, A:H.391, A:N.460 Water bridges: A:N.102, A:D.201, A:D.201, A:D.201, A:E.461, A:F.601 2DG.34: 13 residues within 4Å: Chain B: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604, W.999 Ligands: NA.37 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.102, B:D.201, B:H.391, B:N.460 Water bridges: B:D.201, B:D.201, B:D.201, B:D.201, B:H.418, B:F.601 2DG.68: 13 residues within 4Å: Chain C: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604 Ligands: MG.69, NA.71 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.102, C:H.391, C:Y.503, C:H.540 Water bridges: C:D.201, C:D.201 2DG.103: 12 residues within 4Å: Chain D: D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, N.604 Ligands: MG.104, NA.107 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:H.391, D:N.460, D:Y.503, D:H.540 Water bridges: D:N.102, D:D.201, D:D.201, D:D.201

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

MG.2: 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.3: 8 residues within 4Å: Chain A: D.15, W.16, N.18, P.19, 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.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.35: 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.40, H2O.42, H2O.45 MG.36: 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.69: 4 residues within 4Å: Chain C: E.416, H.418, E.461 Ligands: 2DG.68 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.416, C:H.418, C:E.461, H2O.78, H2O.81, H2O.84 MG.70: 6 residues within 4Å: Chain C: D.15, N.18, V.21, Y.161, 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.104: 6 residues within 4Å: Chain D: N.102, D.201, E.416, H.418, E.461 Ligands: 2DG.103 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.416, D:H.418, D:E.461, H2O.115, H2O.118, H2O.121 MG.105: 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.106: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.5: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: 2DG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.568, A:N.604 NA.6: 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:L.562, A:L.562 NA.7: 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.8: 4 residues within 4Å: Chain A: S.647, E.650, L.670 Ligands: DMS.28 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.650, A:L.670, A:L.670 NA.37: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 2DG.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.201, B:N.604 NA.38: 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:Y.559, B:L.562 NA.39: 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.40: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.647, B:E.650, B:L.670 NA.71: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: 2DG.68 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.100, C:N.604, C:N.604 NA.72: 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:P.560, C:L.562 NA.73: 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:L.967 NA.74: 5 residues within 4Å: Chain C: S.647, D.648, E.650, L.670 Ligands: DMS.95 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.650, C:E.650, C:L.670 NA.107: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: 2DG.103 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.201, D:N.604 NA.108: 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:Y.559, D:L.562 NA.109: 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:M.968

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

DMS.9: 10 residues within 4Å: Chain A: V.227, T.229, V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.10: 6 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718 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: 6 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.14: 5 residues within 4Å: Chain A: E.314, H.316, G.320, T.321, 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: 5 residues within 4Å: Chain A: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: P.106, I.107, P.115, W.191 Ligands: DMS.25 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: 4 residues within 4Å: Chain A: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.23: 2 residues within 4Å: Chain A: K.621, W.717 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain A: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligands: DMS.18 Ligand excluded by PLIP DMS.26: 4 residues within 4Å: Chain A: D.428, P.430 Chain D: W.474, V.478 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.28: 7 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.8 Ligand excluded by PLIP DMS.29: 6 residues within 4Å: Chain A: A.34, W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain A: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain A: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.33: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.41: 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.42: 5 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.44: 7 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain B: G.270, T.271, L.291, R.292 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain B: E.314, H.316, G.320, T.321 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.50: 3 residues within 4Å: Chain B: P.106, P.115, W.191 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.52: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.53: 3 residues within 4Å: Chain B: G.593, D.594, T.595 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.55: 4 residues within 4Å: Chain B: K.621, R.699, I.714, W.717 Ligand excluded by PLIP DMS.56: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.57: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.58: 3 residues within 4Å: Chain B: D.428 Chain C: W.474, V.478 Ligand excluded by PLIP DMS.59: 2 residues within 4Å: Chain B: H.93, Y.95 Ligand excluded by PLIP DMS.60: 5 residues within 4Å: Chain B: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.61: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.40 Ligand excluded by PLIP DMS.62: 2 residues within 4Å: Chain B: Q.719, R.721 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.64: 4 residues within 4Å: Chain B: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.65: 4 residues within 4Å: Chain B: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.66: 4 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.75: 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.76: 6 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.77: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.78: 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.79: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.80: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.81: 5 residues within 4Å: Chain C: L.54, N.55, E.57, W.58, L.125 Ligand excluded by PLIP DMS.82: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.83: 5 residues within 4Å: Chain C: P.106, I.107, P.115, W.191 Ligands: DMS.86 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.85: 4 residues within 4Å: Chain C: G.275, V.289, T.290, R.292 Ligand excluded by PLIP DMS.86: 4 residues within 4Å: Chain C: G.593, D.594, T.595 Ligands: DMS.83 Ligand excluded by PLIP DMS.87: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.88: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.89: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.90: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.91: 6 residues within 4Å: Chain C: T.104, Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain B: R.448 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.93: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.94: 5 residues within 4Å: Chain C: Y.926, P.928, Y.962, R.973, H.974 Ligand excluded by PLIP DMS.95: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, P.703 Ligands: NA.74 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain C: W.695, Q.719, W.720, R.721 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain C: W.36, D.45, R.46, P.47, S.48 Ligand excluded by PLIP DMS.98: 4 residues within 4Å: Chain C: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.99: 4 residues within 4Å: Chain C: R.37, S.132, W.133, H.216 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain C: N.102, D.598, F.601, V.795 Ligand excluded by PLIP DMS.101: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.102: 3 residues within 4Å: Chain C: Q.266, V.267, A.268 Ligand excluded by PLIP DMS.110: 8 residues within 4Å: Chain D: V.227, T.229, V.330, G.331, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.111: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.112: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.113: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.127 Ligand excluded by PLIP DMS.114: 3 residues within 4Å: Chain D: T.271, L.291, R.292 Ligand excluded by PLIP DMS.115: 5 residues within 4Å: Chain D: E.314, H.316, G.320, T.321 Ligands: DMS.130 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain D: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.117: 5 residues within 4Å: Chain D: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.118: 3 residues within 4Å: Chain D: P.106, P.115, W.191 Ligand excluded by PLIP DMS.119: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.120: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.121: 3 residues within 4Å: Chain D: G.593, D.594, T.595 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain D: T.83, V.84, V.85, H.93 Ligand excluded by PLIP DMS.123: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.124: 6 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.125: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.126: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.127: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.113 Ligand excluded by PLIP DMS.128: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.129: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.130: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.115 Ligand excluded by PLIP DMS.131: 4 residues within 4Å: Chain D: Q.49, Q.50, D.130, W.133 Ligand excluded by PLIP DMS.132: 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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