SMTL ID : 3vd3.1

E. coli (lacZ) beta-galactosidase (N460D)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.131, 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.1, H2O.5 MG.17: 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.9, H2O.9, H2O.9 MG.18: 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.34: 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:H.447, C:E.490, H2O.13, H2O.13, H2O.13 MG.35: 6 residues within 4Å: Chain C: D.44, N.47, V.50, Y.190, Q.192, D.222 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.44, C:N.47, C:V.50, C:D.222 MG.51: 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.16, H2O.17, H2O.17 MG.52: 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

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

NA.2: 5 residues within 4Å: Chain A: Y.129, D.230, W.597, F.630, N.633 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.129, A:N.633, A:N.633 Water bridges: A:N.131, A:D.230 NA.3: 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:L.591 NA.4: 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.19: 4 residues within 4Å: Chain B: Y.129, D.230, F.630, N.633 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.129, B:F.630, B:N.633 NA.20: 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:F.585 NA.21: 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:L.996 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.36: 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:D.230, C:N.633 NA.37: 5 residues within 4Å: Chain C: L.379, F.585, Y.588, P.589, L.591 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.589 NA.38: 1 residues within 4Å: Chain C: N.626 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.626, C:N.626 NA.53: 4 residues within 4Å: Chain D: Y.129, D.230, F.630, N.633 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.633 NA.54: 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:L.591

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

DMS.5: 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.6: 6 residues within 4Å: Chain A: R.586, H.651, Q.652, Q.654, Q.657, Q.747 Ligand excluded by PLIP DMS.7: 6 residues within 4Å: Chain A: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.9: 6 residues within 4Å: Chain A: R.534, E.537, P.1030, S.1031, V.1032, Q.1037 Ligand excluded by PLIP DMS.10: 5 residues within 4Å: Chain A: E.363, V.364, R.365, P.509, S.510 Ligand excluded by PLIP DMS.11: 4 residues within 4Å: Chain A: P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.12: 3 residues within 4Å: Chain A: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.13: 4 residues within 4Å: Chain A: A.63, W.65, D.74, R.75 Ligand excluded by PLIP DMS.14: 4 residues within 4Å: Chain A: Q.295, V.296, A.297, S.298 Ligand excluded by PLIP DMS.15: 3 residues within 4Å: Chain A: V.132, H.447, W.1028 Ligand excluded by PLIP DMS.16: 3 residues within 4Å: Chain A: V.113, V.114, H.122 Ligand excluded by PLIP DMS.23: 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.24: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.25: 3 residues within 4Å: Chain B: G.299, L.320, R.321 Ligand excluded by PLIP DMS.26: 6 residues within 4Å: Chain B: R.534, E.537, P.1030, S.1031, V.1032, Q.1037 Ligand excluded by PLIP DMS.27: 4 residues within 4Å: Chain B: L.83, N.84, G.85, W.87 Ligand excluded by PLIP DMS.28: 4 residues within 4Å: Chain B: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.29: 6 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, D.639, R.1002 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain B: D.457, P.459 Chain C: Q.474, W.503, V.507 Ligand excluded by PLIP DMS.31: 3 residues within 4Å: Chain B: H.122, G.123, Y.124 Ligand excluded by PLIP DMS.32: 5 residues within 4Å: Chain B: D.74, R.75, P.76, S.77, L.80 Ligand excluded by PLIP DMS.33: 7 residues within 4Å: Chain B: E.86, W.87, R.88, T.112, S.153, L.154, T.155 Ligand excluded by PLIP DMS.39: 6 residues within 4Å: Chain C: V.256, V.359, G.360, R.362, N.478, P.480 Ligand excluded by PLIP DMS.40: 5 residues within 4Å: Chain C: K.409, N.412, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.41: 6 residues within 4Å: Chain C: P.61, A.63, W.65, D.74, A.356 Ligands: DMS.49 Ligand excluded by PLIP DMS.42: 3 residues within 4Å: Chain C: G.299, L.320, R.321 Ligand excluded by PLIP DMS.43: 6 residues within 4Å: Chain C: R.534, E.537, P.1030, S.1031, V.1032, Q.1037 Ligand excluded by PLIP DMS.44: 3 residues within 4Å: Chain C: E.363, V.364, R.365 Ligand excluded by PLIP DMS.45: 2 residues within 4Å: Chain C: T.155, E.210 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.47: 4 residues within 4Å: Chain C: G.304, V.318, T.319, R.321 Ligand excluded by PLIP DMS.48: 5 residues within 4Å: Chain B: Q.474, W.503, V.507 Chain C: D.457, P.459 Ligand excluded by PLIP DMS.49: 6 residues within 4Å: Chain C: D.74, R.75, P.76, S.77, L.80 Ligands: DMS.41 Ligand excluded by PLIP DMS.50: 3 residues within 4Å: Chain C: L.83, N.84, L.154 Ligand excluded by PLIP DMS.55: 8 residues within 4Å: Chain D: T.258, V.359, G.360, R.362, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.56: 5 residues within 4Å: Chain D: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.57: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.58: 4 residues within 4Å: Chain D: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.59: 3 residues within 4Å: Chain D: R.534, E.537, P.1030 Ligand excluded by PLIP DMS.60: 6 residues within 4Å: Chain D: S.82, L.83, N.84, G.85, W.87, L.154 Ligand excluded by PLIP DMS.61: 4 residues within 4Å: Chain D: E.363, V.364, R.365, P.509 Ligand excluded by PLIP DMS.62: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.63: 5 residues within 4Å: Chain D: G.304, G.305, E.306, V.318, T.319 Ligand excluded by PLIP DMS.64: 1 residues within 4Å: Chain D: V.132 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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