SMTL ID : 3vda.1

E. coli (lacZ) beta-galactosidase (N460T)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.16, H2O.17 MG.2: 5 residues within 4Å: Chain A: D.44, N.47, V.50, Q.192, D.222 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.44, A:N.47, A:V.50, A:D.222 MG.13: 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.31, H2O.32 MG.14: 5 residues within 4Å: Chain B: D.44, N.47, V.50, 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.25: 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.44, H2O.46, H2O.47 MG.26: 6 residues within 4Å: Chain C: D.44, 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.36: 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:E.445, D:E.490, H2O.57, H2O.61, H2O.62 MG.37: 5 residues within 4Å: Chain D: D.44, N.47, V.50, 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.3: 4 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.630, A:N.633 Water bridges: A:N.131 NA.4: 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:P.589 NA.5: 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.15: 4 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230, B:N.633 NA.16: 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:P.589 NA.27: 4 residues within 4Å: Chain C: Y.129, D.230, F.630, N.633 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.633, C:N.633 NA.28: 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.38: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.129, D:N.633, D:N.633 NA.39: 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.40: 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

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

DMS.6: 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.7: 4 residues within 4Å: Chain A: R.586, H.651, Q.654, Q.657 Ligand excluded by PLIP DMS.8: 6 residues within 4Å: Chain A: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.9: 7 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligand excluded by PLIP DMS.10: 3 residues within 4Å: Chain A: G.299, L.320, R.321 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.12: 5 residues within 4Å: Chain A: D.457, P.459 Chain D: H.255, Q.474, V.507 Ligand excluded by PLIP DMS.17: 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.18: 4 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.657 Ligand excluded by PLIP DMS.19: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.20: 7 residues within 4Å: Chain B: P.61, F.62, A.63, W.65, D.74, A.356 Ligands: DMS.24 Ligand excluded by PLIP DMS.21: 5 residues within 4Å: Chain B: G.299, T.300, L.320, R.321, L.322 Ligand excluded by PLIP DMS.22: 4 residues within 4Å: Chain B: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.23: 3 residues within 4Å: Chain B: V.318, T.319, R.321 Ligand excluded by PLIP DMS.24: 5 residues within 4Å: Chain B: W.65, D.74, R.75, P.76 Ligands: DMS.20 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.657 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain C: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain C: R.81, L.83, L.154, T.155, F.156 Ligand excluded by PLIP DMS.33: 4 residues within 4Å: Chain C: G.304, V.318, T.319, R.321 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain C: T.112, V.113, V.114, H.122 Ligand excluded by PLIP DMS.35: 6 residues within 4Å: Chain C: A.63, W.65, D.74, R.75, P.76, S.77 Ligand excluded by PLIP DMS.41: 10 residues within 4Å: Chain D: V.256, T.258, D.358, V.359, G.360, R.362, R.477, N.478, P.480, R.511 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.43: 5 residues within 4Å: Chain D: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.44: 5 residues within 4Å: Chain D: R.534, E.537, P.1030, V.1032, Q.1037 Ligand excluded by PLIP DMS.45: 4 residues within 4Å: Chain D: S.82, L.83, N.84, L.154 Ligand excluded by PLIP DMS.46: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.47: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.48: 4 residues within 4Å: Chain D: G.305, V.318, T.319, R.321 Ligand excluded by PLIP DMS.49: 3 residues within 4Å: Chain D: A.63, D.74, L.80 Ligand excluded by PLIP DMS.50: 5 residues within 4Å: Chain D: G.299, T.319, L.320, R.321, L.322 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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