SMTL ID : 3vdc.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

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

IPT.1: 13 residues within 4Å: Chain A: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.1028 Hydrogen bonds: A:N.131, A:E.490, A:F.630, A:N.633 Water bridges: A:E.566 IPT.17: 13 residues within 4Å: Chain B: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.20 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.1028 Hydrogen bonds: B:N.131, B:D.230, B:E.490, B:F.630, B:N.633 Water bridges: B:D.230, B:H.420, B:E.566 IPT.35: 12 residues within 4Å: Chain C: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, F.630, N.633, W.1028 Ligands: NA.38 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.1028 Hydrogen bonds: C:N.131, C:E.490, C:F.630, C:N.633 IPT.51: 13 residues within 4Å: Chain D: N.131, D.230, H.447, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.54 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.1028 Hydrogen bonds: D:N.131, D:D.230, D:E.490, D:Y.532, D:F.630, D:N.633 Water bridges: D:H.447, D:E.490, D:E.566

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: 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.15, H2O.17, H2O.17 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.18: 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.18, H2O.23, H2O.32 MG.19: 6 residues within 4Å: Chain B: D.44, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.44, B:N.47, B:V.50, B:D.222 MG.36: 3 residues within 4Å: Chain C: E.445, H.447, E.490 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.445, C:H.447, C:E.490, H2O.35, H2O.39, H2O.48 MG.37: 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.52: 3 residues within 4Å: Chain D: E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:H.447, D:E.490, H2O.50, H2O.50, H2O.56 MG.53: 7 residues within 4Å: Chain D: D.44, W.45, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.44, D:N.47, D:V.50, D:D.222

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

NA.4: 6 residues within 4Å: Chain A: Y.129, D.230, W.597, F.630, N.633 Ligands: IPT.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.630, A:N.633 NA.5: 4 residues within 4Å: Chain A: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.585 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:P.961 NA.20: 7 residues within 4Å: Chain B: Y.129, D.230, W.597, F.630, C.631, N.633 Ligands: IPT.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.630, B:N.633 NA.21: 4 residues within 4Å: Chain B: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.588 NA.22: 5 residues within 4Å: Chain B: S.676, D.677, N.678, E.679, L.699 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.676, B:E.679 NA.38: 7 residues within 4Å: Chain C: Y.129, D.230, W.597, F.630, C.631, N.633 Ligands: IPT.35 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.129, C:N.633, C:N.633 NA.39: 4 residues within 4Å: Chain C: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.589 NA.54: 6 residues within 4Å: Chain D: Y.129, D.230, W.597, F.630, N.633 Ligands: IPT.51 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.129, D:W.597, D:N.633 NA.55: 4 residues within 4Å: Chain D: F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.588

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

DMS.7: 8 residues within 4Å: Chain A: V.256, T.258, V.359, G.360, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.8: 5 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: K.409, N.412, F.413, 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.16 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: S.82, L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.15: 7 residues within 4Å: Chain A: D.457, P.459 Chain D: H.255, Q.474, R.477, W.503, V.507 Ligand excluded by PLIP DMS.16: 6 residues within 4Å: Chain A: A.63, D.74, R.75, P.76, L.80 Ligands: DMS.10 Ligand excluded by PLIP DMS.23: 8 residues within 4Å: Chain B: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.24: 4 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.657 Ligand excluded by PLIP DMS.25: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.26: 7 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.33 Ligand excluded by PLIP DMS.27: 5 residues within 4Å: Chain B: G.299, T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.28: 5 residues within 4Å: Chain B: T.286, E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain B: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain B: L.83, N.84, E.86, L.154, F.156 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain B: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain B: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.33: 6 residues within 4Å: Chain B: W.65, D.74, R.75, P.76, S.77 Ligands: DMS.26 Ligand excluded by PLIP DMS.34: 6 residues within 4Å: Chain B: E.86, W.87, R.88, S.153, L.154, T.155 Ligand excluded by PLIP DMS.40: 8 residues within 4Å: Chain C: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.43: 8 residues within 4Å: Chain C: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.49 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain C: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain C: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.46: 7 residues within 4Å: Chain C: R.81, S.82, L.83, N.84, L.154, T.155, F.156 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain C: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain C: G.304, G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.49: 4 residues within 4Å: Chain C: D.74, P.76, L.80 Ligands: DMS.43 Ligand excluded by PLIP DMS.50: 3 residues within 4Å: Chain B: H.255, R.477 Chain C: D.457 Ligand excluded by PLIP DMS.56: 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.57: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.58: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.59: 8 residues within 4Å: Chain D: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.67 Ligand excluded by PLIP DMS.60: 4 residues within 4Å: Chain D: S.298, G.299, L.320, R.321 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain D: S.82, L.83, N.84, L.154, F.156 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.64: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.65: 5 residues within 4Å: Chain D: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.66: 3 residues within 4Å: Chain D: T.647, K.650, W.746 Ligand excluded by PLIP DMS.67: 5 residues within 4Å: Chain D: D.74, R.75, P.76, L.80 Ligands: DMS.59 Ligand excluded by PLIP DMS.68: 2 residues within 4Å: Chain D: R.66, N.67 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

Related Entries With Identical Sequence