SMTL ID : 1jz5.1

E. COLI (lacZ) BETA-GALACTOSIDASE IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ON

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x 149: D-galactonolactone(Non-covalent)

149.1: 13 residues within 4Å: Chain A: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.5 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.102, A:D.201, A:H.391, A:N.460, A:E.461 Water bridges: A:D.201, A:E.461, A:E.461 149.29: 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, F.601, N.604 Ligands: NA.33 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.102, B:D.201, B:H.391, B:N.460, B:E.461 Water bridges: B:D.201, B:D.201, B:D.201 149.59: 14 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, F.601, N.604 Ligands: NA.62, DMS.85 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.102, C:H.391, C:N.460, C:E.461 Water bridges: C:D.201, C:D.201, C:D.201 149.88: 13 residues within 4Å: Chain D: N.102, D.201, H.391, N.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604 Ligands: NA.92 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:H.391, D:N.460, D:E.461 Water bridges: D:D.201, D:D.201, D:D.201

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

MG.2: 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.3: 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.4: 1 residues within 4Å: Ligands: DMS.14 No protein-ligand interaction detected (PLIP) MG.30: 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.38, H2O.41, H2O.44 MG.31: 6 residues within 4Å: Chain B: D.15, W.16, 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.32: 2 residues within 4Å: Chain B: Q.718, T.911 No protein-ligand interaction detected (PLIP) MG.60: 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.75, H2O.77, H2O.80 MG.61: 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.89: 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.112, H2O.114, H2O.117 MG.90: 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 MG.91: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.5: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: 149.1 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: 5 residues within 4Å: Chain A: S.647, N.649, E.650, L.670 Ligands: DMS.24 Ligand excluded by PLIP NA.33: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 149.29 Ligand excluded by PLIP NA.34: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.35: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.36: 4 residues within 4Å: Chain B: S.647, E.650, L.670 Ligands: DMS.54 Ligand excluded by PLIP NA.62: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: 149.59 Ligand excluded by PLIP NA.63: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.64: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.65: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.84 Ligand excluded by PLIP NA.92: 5 residues within 4Å: Chain D: Y.100, D.201, F.601, N.604 Ligands: 149.88 Ligand excluded by PLIP NA.93: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.94: 4 residues within 4Å: Chain D: F.931, P.932, L.967, T.970 Ligand excluded by PLIP NA.95: 5 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligand excluded by PLIP

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

DMS.9: 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.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, W.36, D.45, R.310, A.327 Ligands: DMS.25 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: 6 residues within 4Å: Chain A: E.314, H.316, G.320, T.321, L.322 Ligands: MG.4 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: E.508, P.1001, V.1003, Q.1008 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: L.54, N.55, G.56, 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: 4 residues within 4Å: Chain A: I.576, W.585, S.586, R.973 Ligand excluded by PLIP DMS.19: 6 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.20: 3 residues within 4Å: Chain A: V.84, V.85, H.93 Ligand excluded by PLIP DMS.21: 2 residues within 4Å: Chain A: R.251, D.252 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.24: 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.25: 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.26: 3 residues within 4Å: Chain A: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain A: R.37, W.133, E.136, H.216 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.37: 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.38: 6 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.40: 6 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, A.327 Ligand excluded by PLIP DMS.41: 4 residues within 4Å: Chain B: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain B: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain B: L.54, N.55, G.56, E.57 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: E.334, V.335, R.336, P.480, S.481 Ligand excluded by PLIP DMS.45: 3 residues within 4Å: Chain B: P.106, P.115, W.191 Ligand excluded by PLIP DMS.46: 2 residues within 4Å: Chain B: S.586, R.973 Ligand excluded by PLIP DMS.47: 6 residues within 4Å: Chain B: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.48: 3 residues within 4Å: Chain B: V.84, V.85, H.93 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain B: L.250, R.251, D.252 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: F.231, N.232, D.233, F.235, E.334 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: D.428, P.430 Chain C: H.226, R.288, R.448 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain B: Y.926, P.928, Y.962, R.973 Ligand excluded by PLIP DMS.54: 7 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, P.703, N.704 Ligands: NA.36 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.57: 4 residues within 4Å: Chain B: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain B: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.66: 9 residues within 4Å: Chain C: V.227, T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.67: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain C: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.69: 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.70: 4 residues within 4Å: Chain C: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.73: 4 residues within 4Å: Chain C: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.74: 5 residues within 4Å: Chain C: I.99, P.106, I.107, P.115, W.191 Ligand excluded by PLIP DMS.75: 5 residues within 4Å: Chain C: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.76: 5 residues within 4Å: Chain C: G.275, G.276, V.289, T.290, R.292 Ligand excluded by PLIP DMS.77: 3 residues within 4Å: Chain C: V.84, V.85, H.93 Ligand excluded by PLIP DMS.78: 3 residues within 4Å: Chain C: K.621, I.714, W.717 Ligand excluded by PLIP DMS.79: 3 residues within 4Å: Chain C: L.250, R.251, D.252 Ligand excluded by PLIP DMS.80: 6 residues within 4Å: Chain C: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.81: 3 residues within 4Å: Chain B: W.474 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.82: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.83: 5 residues within 4Å: Chain C: Y.926, Y.962, R.973, H.974, L.976 Ligand excluded by PLIP DMS.84: 5 residues within 4Å: Chain C: S.647, D.648, N.649, E.650 Ligands: NA.65 Ligand excluded by PLIP DMS.85: 3 residues within 4Å: Chain C: N.102, W.999 Ligands: 149.59 Ligand excluded by PLIP DMS.86: 5 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain C: V.267, N.294, V.295, E.296 Ligand excluded by PLIP DMS.96: 9 residues within 4Å: Chain D: V.227, T.229, V.330, G.331, R.333, R.448, N.449, P.451, R.482 Ligand excluded by PLIP DMS.97: 5 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628 Ligand excluded by PLIP DMS.98: 5 residues within 4Å: Chain D: K.380, N.383, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.99: 7 residues within 4Å: Chain D: P.32, F.33, W.36, D.45, R.310, A.327 Ligands: DMS.113 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain D: T.271, T.290, L.291, R.292 Ligand excluded by PLIP DMS.101: 4 residues within 4Å: Chain D: E.314, H.316, G.320 Ligands: DMS.116 Ligand excluded by PLIP DMS.102: 6 residues within 4Å: Chain D: S.53, L.54, N.55, G.56, E.57, L.125 Ligand excluded by PLIP DMS.103: 3 residues within 4Å: Chain D: E.334, V.335, R.336 Ligand excluded by PLIP DMS.104: 3 residues within 4Å: Chain D: P.106, P.115, W.191 Ligand excluded by PLIP DMS.105: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.106: 6 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.107: 3 residues within 4Å: Chain D: V.84, V.85, H.93 Ligand excluded by PLIP DMS.108: 3 residues within 4Å: Chain D: L.250, R.251, D.252 Ligand excluded by PLIP DMS.109: 6 residues within 4Å: Chain D: F.231, N.232, D.233, F.235, E.334, R.336 Ligand excluded by PLIP DMS.110: 5 residues within 4Å: Chain D: Y.105, P.106, I.107, T.108, P.596 Ligand excluded by PLIP DMS.111: 3 residues within 4Å: Chain D: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.112: 4 residues within 4Å: Chain D: Y.926, Y.962, R.973, L.976 Ligand excluded by PLIP DMS.113: 6 residues within 4Å: Chain D: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.99 Ligand excluded by PLIP DMS.114: 4 residues within 4Å: Chain D: F.629, R.630, Q.718, W.720 Ligand excluded by PLIP DMS.115: 4 residues within 4Å: Chain D: S.923, Y.926, R.961, Y.962 Ligand excluded by PLIP DMS.116: 3 residues within 4Å: Chain D: G.320, L.322 Ligands: DMS.101 Ligand excluded by PLIP DMS.117: 4 residues within 4Å: Chain D: Q.49, Q.50, D.130, W.133 Ligand excluded by PLIP DMS.118: 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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