SMTL ID : 3czj.2 (1 other biounit)

E. COLI (lacZ) BETA-GALACTOSIDASE (N460T) IN COMPLEX WITH D-GALCTOPYRANOSYL-1-ONE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

149.1: 15 residues within 4Å: Chain A: N.102, D.201, H.391, T.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.4, DMS.25 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.102, A:H.391, A:T.460, A:E.461 Water bridges: A:D.201, A:D.201, A:D.201 149.32: 15 residues within 4Å: Chain B: N.102, D.201, H.391, T.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.36, DMS.58 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.102, B:D.201, B:H.391, B:T.460, B:E.461 Water bridges: B:D.201, B:D.201, B:D.201 149.66: 15 residues within 4Å: Chain C: N.102, D.201, H.391, T.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.69, DMS.93 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.102, C:H.391, C:E.461 Water bridges: C:D.201, C:D.201, C:D.201 149.98: 15 residues within 4Å: Chain D: N.102, D.201, H.391, T.460, E.461, M.502, Y.503, E.537, H.540, W.568, F.601, N.604, W.999 Ligands: NA.101, DMS.121 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.102, D:D.201, D:H.391, D:E.461 Water bridges: D:D.201, D:D.201, D:D.201

9 x MG: MAGNESIUM ION(Non-covalent)

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.22 MG.3: 5 residues within 4Å: Chain A: D.15, N.18, 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.33: 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.26, H2O.28, H2O.31 MG.34: 6 residues within 4Å: Chain B: D.15, W.16, N.18, V.21, Q.163, D.193 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.15, B:N.18, B:V.21, B:D.193 MG.35: 1 residues within 4Å: Chain B: E.369 No protein-ligand interaction detected (PLIP) MG.67: 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.51, H2O.54, H2O.57 MG.68: 6 residues within 4Å: Chain C: D.15, N.18, V.21, Y.161, Q.163, D.193 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.15, C:N.18, C:V.21, C:D.193, C:D.193 MG.99: 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.79, H2O.81, H2O.84 MG.100: 6 residues within 4Å: Chain D: D.15, N.18, V.21, Y.161, 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

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

NA.4: 5 residues within 4Å: Chain A: Y.100, D.201, F.601, N.604 Ligands: 149.1 Ligand excluded by PLIP NA.5: 4 residues within 4Å: Chain A: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.6: 5 residues within 4Å: Chain A: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.7: 5 residues within 4Å: Chain A: S.647, D.648, N.649, E.650, L.670 Ligand excluded by PLIP NA.36: 5 residues within 4Å: Chain B: Y.100, D.201, F.601, N.604 Ligands: 149.32 Ligand excluded by PLIP NA.37: 4 residues within 4Å: Chain B: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.38: 5 residues within 4Å: Chain B: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.39: 6 residues within 4Å: Chain B: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.55 Ligand excluded by PLIP NA.69: 5 residues within 4Å: Chain C: Y.100, D.201, F.601, N.604 Ligands: 149.66 Ligand excluded by PLIP NA.70: 4 residues within 4Å: Chain C: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.71: 5 residues within 4Å: Chain C: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.72: 6 residues within 4Å: Chain C: S.647, D.648, N.649, E.650, L.670 Ligands: DMS.90 Ligand excluded by PLIP NA.101: 4 residues within 4Å: Chain D: D.201, F.601, N.604 Ligands: 149.98 Ligand excluded by PLIP NA.102: 4 residues within 4Å: Chain D: F.556, Y.559, P.560, L.562 Ligand excluded by PLIP NA.103: 5 residues within 4Å: Chain D: F.931, P.932, L.967, M.968, T.970 Ligand excluded by PLIP NA.104: 5 residues within 4Å: Chain D: S.647, D.648, N.649, E.650, L.670 Ligand excluded by PLIP

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

DMS.8: 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.9: 6 residues within 4Å: Chain A: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.10: 6 residues within 4Å: Chain A: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.11: 8 residues within 4Å: Chain A: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.22 Ligand excluded by PLIP DMS.12: 4 residues within 4Å: Chain A: G.270, T.271, R.292, L.293 Ligand excluded by PLIP DMS.13: 6 residues within 4Å: Chain A: R.505, E.508, P.1001, S.1002, V.1003, Q.1008 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: L.54, N.55, L.125, F.127 Ligand excluded by PLIP DMS.15: 4 residues within 4Å: Chain A: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: I.99, P.106, I.107, P.115, W.191 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.18: 5 residues within 4Å: Chain A: G.275, G.276, E.277, V.289, T.290 Ligand excluded by PLIP DMS.19: 3 residues within 4Å: Chain A: G.593, D.594, T.595 Ligand excluded by PLIP DMS.20: 4 residues within 4Å: Chain A: K.621, R.699, I.714, W.717 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.22: 5 residues within 4Å: Chain A: A.34, W.36, D.45, R.46 Ligands: DMS.11 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain A: E.57, W.58, R.59, L.125, T.126 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain A: Q.266, V.267, A.268, S.269 Ligand excluded by PLIP DMS.25: 5 residues within 4Å: Chain A: N.102, H.418, F.601, W.999 Ligands: 149.1 Ligand excluded by PLIP DMS.26: 5 residues within 4Å: Chain A: T.257, E.314, H.316, G.320, L.322 Ligand excluded by PLIP DMS.27: 3 residues within 4Å: Chain A: I.107, T.108, P.596 Ligand excluded by PLIP DMS.28: 7 residues within 4Å: Chain A: F.60, A.61, W.62, E.80, A.81, D.82, Y.95 Ligand excluded by PLIP DMS.29: 5 residues within 4Å: Chain A: R.37, S.132, W.133, E.136, H.216 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain A: R.282, G.283, G.284, A.286 Chain D: V.421 Ligand excluded by PLIP DMS.31: 7 residues within 4Å: Chain A: H.226, Q.445, R.448, W.474, V.478 Chain D: D.428, P.430 Ligand excluded by PLIP DMS.40: 8 residues within 4Å: Chain B: V.330, G.331, R.333, R.448, N.449, H.450, P.451, R.482 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain B: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.42: 6 residues within 4Å: Chain B: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.43: 9 residues within 4Å: Chain B: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.56, DMS.59 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain B: G.270, T.271, L.291, R.292, L.293 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain B: T.257, E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain B: R.505, E.508, P.1001, S.1002, V.1003 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain B: S.53, L.54, N.55, E.57, L.125 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain B: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain B: I.99, P.106, I.107 Ligand excluded by PLIP DMS.50: 4 residues within 4Å: Chain B: P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.51: 5 residues within 4Å: Chain B: G.275, E.277, V.289, T.290, R.292 Ligand excluded by PLIP DMS.52: 3 residues within 4Å: Chain B: G.593, D.594, T.595 Ligand excluded by PLIP DMS.53: 4 residues within 4Å: Chain B: D.428, P.430 Chain C: W.474, V.478 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.55: 5 residues within 4Å: Chain B: D.648, N.649, E.650, P.703 Ligands: NA.39 Ligand excluded by PLIP DMS.56: 6 residues within 4Å: Chain B: W.36, D.45, R.46, P.47, S.48 Ligands: DMS.43 Ligand excluded by PLIP DMS.57: 6 residues within 4Å: Chain B: E.57, W.58, R.59, S.124, L.125, T.126 Ligand excluded by PLIP DMS.58: 6 residues within 4Å: Chain B: N.102, V.103, H.418, S.796, W.999 Ligands: 149.32 Ligand excluded by PLIP DMS.59: 4 residues within 4Å: Chain B: P.396, L.397, T.400 Ligands: DMS.43 Ligand excluded by PLIP DMS.60: 2 residues within 4Å: Chain B: S.53, N.55 Ligand excluded by PLIP DMS.61: 2 residues within 4Å: Chain B: S.923, Y.962 Ligand excluded by PLIP DMS.62: 3 residues within 4Å: Chain B: I.305, P.306, N.307 Ligand excluded by PLIP DMS.63: 6 residues within 4Å: Chain B: F.60, A.61, W.62, E.80, A.81, D.82 Ligand excluded by PLIP DMS.64: 2 residues within 4Å: Chain B: E.41, P.47 Ligand excluded by PLIP DMS.65: 6 residues within 4Å: Chain B: L.377, T.706, A.707, W.708, S.709, E.710 Ligand excluded by PLIP DMS.73: 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.74: 5 residues within 4Å: Chain C: R.557, H.622, Q.623, Q.628, Q.718 Ligand excluded by PLIP DMS.75: 6 residues within 4Å: Chain C: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.76: 8 residues within 4Å: Chain C: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.91 Ligand excluded by PLIP DMS.77: 3 residues within 4Å: Chain C: T.271, L.291, R.292 Ligand excluded by PLIP DMS.78: 5 residues within 4Å: Chain C: E.314, H.316, G.320, T.321, L.322 Ligand excluded by PLIP DMS.79: 4 residues within 4Å: Chain C: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.80: 7 residues within 4Å: Chain C: S.53, L.54, N.55, E.57, W.58, L.125, F.127 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, W.191 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: 5 residues within 4Å: Chain C: G.275, G.276, E.277, V.289, T.290 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, R.699, W.717 Ligand excluded by PLIP DMS.87: 4 residues within 4Å: Chain B: W.474, V.478 Chain C: D.428, P.430 Ligand excluded by PLIP DMS.88: 3 residues within 4Å: Chain C: H.93, G.94, Y.95 Ligand excluded by PLIP DMS.89: 4 residues within 4Å: Chain C: P.788, K.811, Y.816, M.968 Ligand excluded by PLIP DMS.90: 5 residues within 4Å: Chain C: D.648, N.649, E.650, P.703 Ligands: NA.72 Ligand excluded by PLIP DMS.91: 6 residues within 4Å: Chain C: A.34, W.36, D.45, R.46, P.47 Ligands: DMS.76 Ligand excluded by PLIP DMS.92: 3 residues within 4Å: Chain C: F.629, Q.718, W.720 Ligand excluded by PLIP DMS.93: 6 residues within 4Å: Chain C: N.102, V.103, H.418, E.461, S.796 Ligands: 149.66 Ligand excluded by PLIP DMS.94: 3 residues within 4Å: Chain C: I.305, P.306, N.307 Ligand excluded by PLIP DMS.95: 5 residues within 4Å: Chain C: F.608, D.610, T.612, P.928, R.973 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain C: P.47, S.48, Q.49, L.51 Ligand excluded by PLIP DMS.97: 2 residues within 4Å: Chain C: R.13, H.151 Ligand excluded by PLIP DMS.105: 6 residues within 4Å: Chain A: D.428, P.430, A.466 Chain D: Q.445, W.474, V.478 Ligand excluded by PLIP DMS.106: 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.107: 6 residues within 4Å: Chain D: R.557, H.622, Q.623, Q.625, Q.628, Q.718 Ligand excluded by PLIP DMS.108: 6 residues within 4Å: Chain D: K.380, N.383, F.384, F.626, Y.642, W.708 Ligand excluded by PLIP DMS.109: 8 residues within 4Å: Chain D: P.32, F.33, A.34, W.36, D.45, R.310, A.327 Ligands: DMS.120 Ligand excluded by PLIP DMS.110: 4 residues within 4Å: Chain D: G.270, T.271, R.292, L.293 Ligand excluded by PLIP DMS.111: 4 residues within 4Å: Chain D: R.505, E.508, P.1001, V.1003 Ligand excluded by PLIP DMS.112: 5 residues within 4Å: Chain D: S.53, L.54, N.55, G.56, L.125 Ligand excluded by PLIP DMS.113: 4 residues within 4Å: Chain D: E.334, V.335, R.336, P.480 Ligand excluded by PLIP DMS.114: 3 residues within 4Å: Chain D: P.106, P.115, E.117 Ligand excluded by PLIP DMS.115: 5 residues within 4Å: Chain D: I.576, P.584, W.585, S.586, R.973 Ligand excluded by PLIP DMS.116: 5 residues within 4Å: Chain D: G.275, G.276, E.277, V.289, T.290 Ligand excluded by PLIP DMS.117: 3 residues within 4Å: Chain D: V.84, V.85, H.93 Ligand excluded by PLIP DMS.118: 4 residues within 4Å: Chain D: K.621, R.699, I.714, W.717 Ligand excluded by PLIP DMS.119: 4 residues within 4Å: Chain D: F.231, N.232, D.233, E.334 Ligand excluded by PLIP DMS.120: 5 residues within 4Å: Chain D: D.45, R.46, P.47, L.51 Ligands: DMS.109 Ligand excluded by PLIP DMS.121: 5 residues within 4Å: Chain D: H.418, E.461, S.796, W.999 Ligands: 149.98 Ligand excluded by PLIP DMS.122: 4 residues within 4Å: Chain D: Y.472, T.494, T.496, D.497 Ligand excluded by PLIP DMS.123: 3 residues within 4Å: Chain D: L.341, G.346, P.348 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kappelhoff, J.C. et al., Practical Considerations When Using Temperature to Obtain Rate Constants and Activation Thermodynamics of Enzymes with Two Catalytic Steps: Native and N460T-beta-Galactosidase (E. coli) as Examples. Protein J. (2009)

Release Date

2009-04-07

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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