SMTL ID : 3vd5.1

E. coli (lacZ) beta-galactosidase (N460S)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.131, D.230, E.445, H.447, E.490 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.445, A:H.447, A:E.490, H2O.2, H2O.8 MG.2: 6 residues within 4Å: Chain A: D.44, N.47, V.50, Y.190, 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.14: 3 residues within 4Å: Chain B: E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.447, B:E.490, H2O.13, H2O.17, H2O.19 MG.15: 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.25: 3 residues within 4Å: Chain C: E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.445, C:H.447, H2O.26, H2O.29, H2O.29 MG.26: 5 residues within 4Å: Chain C: D.44, N.47, V.50, 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.35: 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.32, H2O.35, H2O.39 MG.36: 6 residues within 4Å: Chain D: D.44, 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

11 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:Y.129, A:Y.129, A:N.633 NA.4: 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:P.589 Water bridges: A:Q.592 NA.5: 5 residues within 4Å: Chain A: F.960, P.961, L.996, M.997, T.999 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.996, A:T.999 NA.16: 5 residues within 4Å: Chain B: Y.129, D.230, W.597, F.630, N.633 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.129, B:N.633 NA.17: 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.18: 5 residues within 4Å: Chain B: F.960, P.961, L.996, M.997, T.999 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.997, B:T.999 NA.27: 5 residues within 4Å: Chain C: Y.129, D.230, F.630, C.631, 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 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.588, C:L.591 NA.37: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.129, D:W.597, D:N.633 Water bridges: D:N.131 NA.38: 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 NA.39: 3 residues within 4Å: Chain D: S.676, E.679, L.699 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.676, D:E.679, D:L.699

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

DMS.6: 5 residues within 4Å: Chain A: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.7: 4 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.657 Ligand excluded by PLIP DMS.8: 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.9: 4 residues within 4Å: Chain A: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.10: 7 residues within 4Å: Chain A: A.63, W.65, D.74, R.75, P.76, S.77 Ligands: DMS.12 Ligand excluded by PLIP DMS.11: 5 residues within 4Å: Chain A: E.86, W.87, R.88, L.154, T.155 Ligand excluded by PLIP DMS.12: 8 residues within 4Å: Chain A: P.61, F.62, A.63, W.65, D.74, R.339, A.356 Ligands: DMS.10 Ligand excluded by PLIP DMS.13: 1 residues within 4Å: Chain A: V.98 Ligand excluded by PLIP DMS.19: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.20: 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.21: 3 residues within 4Å: Chain B: G.304, V.318, T.319 Ligand excluded by PLIP DMS.22: 7 residues within 4Å: Chain B: R.586, H.651, Q.652, Q.654, F.656, Q.657, Q.747 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain B: F.658, R.659, Q.747, W.749 Ligand excluded by PLIP DMS.24: 2 residues within 4Å: Chain B: D.74, S.77 Ligand excluded by PLIP DMS.29: 4 residues within 4Å: Chain C: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain C: G.299, T.319, L.320, R.321, L.322 Ligand excluded by PLIP DMS.31: 4 residues within 4Å: Chain C: D.74, R.75, P.76, L.80 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain C: L.83, N.84, G.85, E.86, L.154 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.657, Q.747 Ligand excluded by PLIP DMS.34: 4 residues within 4Å: Chain C: R.259, F.260, R.266, V.268 Ligand excluded by PLIP DMS.40: 4 residues within 4Å: Chain D: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.42: 5 residues within 4Å: Chain D: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.43: 7 residues within 4Å: Chain D: V.256, T.258, V.359, G.360, R.477, N.478, P.480 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
C

C
D

D
B

Beta-galactosidase

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