SMTL ID : 3vdb.1

E. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

149.1: 14 residues within 4Å: Chain A: N.131, D.230, H.420, T.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633 Ligands: NA.4, DMS.20 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.420, A:T.489, A:E.490 Water bridges: A:N.131, A:D.230, A:D.230, A:E.490 149.25: 15 residues within 4Å: Chain B: N.131, D.230, H.420, T.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.29, DMS.50 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.230, B:H.420, B:T.489, B:E.490 Water bridges: B:D.230, B:D.230, B:D.230 149.57: 15 residues within 4Å: Chain C: N.131, D.230, H.420, T.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.60, DMS.78 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.131, C:H.420, C:E.490 Water bridges: C:D.230, C:D.230, C:D.230 149.84: 15 residues within 4Å: Chain D: N.131, D.230, H.420, T.489, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.87, DMS.103 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.230, D:H.420, D:E.490 Water bridges: D:D.230, D:D.230, D:E.490

9 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: N.131, E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.445, A:H.447, A:E.490, H2O.25, H2O.27, H2O.29 MG.3: 5 residues within 4Å: Chain A: D.44, N.47, V.50, Q.192, D.222 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.44, A:N.47, A:V.50, A:D.222, A:D.222 MG.26: 3 residues within 4Å: Chain B: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.445, B:H.447, B:E.490, H2O.39, H2O.59, H2O.61 MG.27: 5 residues within 4Å: Chain B: D.44, N.47, V.50, Q.192, D.222 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.44, B:N.47, B:V.50, B:D.222, B:D.222 MG.28: 1 residues within 4Å: Chain B: E.398 No protein-ligand interaction detected (PLIP) MG.58: 5 residues within 4Å: Chain C: N.131, D.228, E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.445, C:E.490, H2O.94, H2O.99, H2O.102 MG.59: 7 residues within 4Å: Chain C: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:D.44, C:N.47, C:V.50, C:D.222, C:D.222 MG.85: 3 residues within 4Å: Chain D: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.445, D:H.447, D:E.490, H2O.104, H2O.128, H2O.133 MG.86: 6 residues within 4Å: Chain D: D.44, N.47, V.50, Y.190, Q.192, D.222 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:D.44, D:N.47, D:V.50, D:D.222, D:D.222

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

NA.4: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: 149.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.230, A:N.633 NA.5: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.585, A:L.591 NA.6: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.996 NA.29: 5 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 Ligands: 149.25 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230, B:N.633 NA.30: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.585, B:L.591 NA.31: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.961 NA.32: 6 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 Ligands: DMS.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.676, B:E.679, B:L.699 NA.60: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 Ligands: 149.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.129, C:Y.129, C:N.633 NA.61: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.591, C:L.591 NA.62: 5 residues within 4Å: Chain C: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:M.997 NA.87: 6 residues within 4Å: Chain D: Y.129, D.230, W.597, F.630, N.633 Ligands: 149.84 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.230, D:N.633 NA.88: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:P.589, D:L.591 NA.89: 5 residues within 4Å: Chain D: F.960, P.961, L.996, M.997, T.999 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:M.997 NA.90: 5 residues within 4Å: Chain D: S.676, D.677, N.678, E.679, L.699 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.679, D:E.679

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

DMS.7: 8 residues within 4Å: Chain A: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.9: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.10: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.17 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.15: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.16: 5 residues within 4Å: Chain A: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.17: 5 residues within 4Å: Chain A: A.63, W.65, D.74, R.75 Ligands: DMS.10 Ligand excluded by PLIP DMS.18: 3 residues within 4Å: Chain A: E.86, L.154, T.155 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.20: 6 residues within 4Å: Chain A: N.131, V.132, H.447, S.825, W.1028 Ligands: 149.1 Ligand excluded by PLIP DMS.21: 3 residues within 4Å: Chain A: P.135, T.137, P.625 Ligand excluded by PLIP DMS.22: 7 residues within 4Å: Chain A: F.89, A.90, W.91, E.109, A.110, D.111, Y.124 Ligand excluded by PLIP DMS.23: 5 residues within 4Å: Chain A: R.311, G.312, G.313, A.315 Chain D: V.450 Ligand excluded by PLIP DMS.24: 6 residues within 4Å: Chain A: H.255, Q.474, R.477, W.503, V.507 Chain D: D.457 Ligand excluded by PLIP DMS.33: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.34: 6 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.35: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.36: 9 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.48, DMS.51 Ligand excluded by PLIP DMS.37: 5 residues within 4Å: Chain B: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.38: 5 residues within 4Å: Chain B: T.286, E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.39: 5 residues within 4Å: Chain B: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain B: L.83, N.84, E.86, L.154, F.156 Ligand excluded by PLIP DMS.41: 5 residues within 4Å: Chain B: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.42: 4 residues within 4Å: Chain B: I.128, P.135, I.136, P.144 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.44: 6 residues within 4Å: Chain B: G.304, G.305, E.306, V.318, T.319, R.321 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain B: E.773, M.774, R.789, Q.790 Ligand excluded by PLIP DMS.46: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain B: D.677, N.678, E.679 Ligands: NA.32 Ligand excluded by PLIP DMS.48: 8 residues within 4Å: Chain B: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.36, DMS.51 Ligand excluded by PLIP DMS.49: 5 residues within 4Å: Chain B: E.86, W.87, S.153, L.154, T.155 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain B: N.131, V.132, S.825, W.1028 Ligands: 149.25 Ligand excluded by PLIP DMS.51: 6 residues within 4Å: Chain B: P.61, P.425, L.426, T.429 Ligands: DMS.36, DMS.48 Ligand excluded by PLIP DMS.52: 1 residues within 4Å: Chain B: S.82 Ligand excluded by PLIP DMS.53: 2 residues within 4Å: Chain B: S.952, Y.991 Ligand excluded by PLIP DMS.54: 3 residues within 4Å: Chain B: I.334, P.335, N.336 Ligand excluded by PLIP DMS.55: 6 residues within 4Å: Chain B: F.89, A.90, W.91, E.109, A.110, D.111 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.63: 9 residues within 4Å: Chain C: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.64: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.65: 6 residues within 4Å: Chain C: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.66: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.77 Ligand excluded by PLIP DMS.67: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.68: 5 residues within 4Å: Chain C: E.343, H.345, G.349, T.350, L.351 Ligand excluded by PLIP DMS.69: 4 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.70: 8 residues within 4Å: Chain C: S.82, L.83, N.84, G.85, E.86, W.87, L.154, F.156 Ligand excluded by PLIP DMS.71: 4 residues within 4Å: Chain C: E.363, V.364, P.509, S.510 Ligand excluded by PLIP DMS.72: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.73: 5 residues within 4Å: Chain C: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.74: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.75: 4 residues within 4Å: Chain B: W.503, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.76: 4 residues within 4Å: Chain C: D.111, H.122, G.123, Y.124 Ligand excluded by PLIP DMS.77: 6 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76 Ligands: DMS.66 Ligand excluded by PLIP DMS.78: 5 residues within 4Å: Chain C: N.131, V.132, S.825, W.1028 Ligands: 149.57 Ligand excluded by PLIP DMS.79: 3 residues within 4Å: Chain C: I.334, P.335, N.336 Ligand excluded by PLIP DMS.80: 5 residues within 4Å: Chain C: F.637, D.639, T.641, P.957, R.1002 Ligand excluded by PLIP DMS.81: 3 residues within 4Å: Chain C: L.279, R.280, D.281 Ligand excluded by PLIP DMS.82: 4 residues within 4Å: Chain C: S.77, Q.78, L.80, R.81 Ligand excluded by PLIP DMS.83: 6 residues within 4Å: Chain A: D.457, P.459 Chain D: H.255, Q.474, W.503, V.507 Ligand excluded by PLIP DMS.91: 9 residues within 4Å: Chain D: T.258, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.92: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.93: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.94: 8 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.102 Ligand excluded by PLIP DMS.95: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.96: 4 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.97: 6 residues within 4Å: Chain D: S.82, L.83, N.84, E.86, W.87, L.154 Ligand excluded by PLIP DMS.98: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.99: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.100: 4 residues within 4Å: Chain D: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.101: 4 residues within 4Å: Chain D: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.102: 6 residues within 4Å: Chain D: A.63, D.74, R.75, P.76, L.80 Ligands: DMS.94 Ligand excluded by PLIP DMS.103: 5 residues within 4Å: Chain D: N.131, V.132, H.447, S.825 Ligands: 149.84 Ligand excluded by PLIP DMS.104: 5 residues within 4Å: Chain D: Y.501, T.523, T.525, D.526, R.560 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wheatley, R.W. et al., Substitution for Asn460 cripples {beta}-galactosidase (Escherichia coli) by increasing substrate affinity and decreasing transition state stability. Arch.Biochem.Biophys. (2012)

Release Date

2012-04-11

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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