SMTL ID : 3vd7.1

E. coli (lacZ) beta-galactosidase (N460S) in complex with galactotetrazole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.87 Å

Oligo State

homo-tetramer

Ligands

4 x GTZ: (5R, 6S, 7S, 8S)-5-HYDROXYMETHYL-6,7,8-TRIHYDROXY-TETRAZOLO[1,5-A]PIPERIDINE(Non-covalent)

GTZ.1: 14 residues within 4Å: Chain A: N.131, D.230, H.420, H.447, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.3 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.131, A:D.230, A:E.490, A:Y.532, A:E.566, A:F.630 Water bridges: A:D.230, A:H.420, A:H.447, A:H.447 pi-Stacking: A:W.1028 GTZ.11: 12 residues within 4Å: Chain B: N.131, D.230, H.420, E.490, M.531, Y.532, E.566, H.569, W.597, N.633, W.1028 Ligands: NA.14 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.490, B:E.566, B:F.630 Water bridges: B:N.131, B:N.131, B:D.230, B:H.420 pi-Stacking: B:W.1028 GTZ.24: 13 residues within 4Å: Chain C: N.131, D.230, H.420, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.27 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.490, C:E.566, C:F.630 Water bridges: C:D.230, C:H.420, C:H.447, C:H.447 pi-Stacking: C:W.1028 GTZ.37: 13 residues within 4Å: Chain D: D.230, H.420, H.447, E.490, M.531, Y.532, E.566, H.569, W.597, F.630, N.633, W.1028 Ligands: NA.39 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.230, D:E.490, D:E.566, D:F.630 pi-Stacking: D:W.1028

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.3, H2O.3 MG.12: 5 residues within 4Å: Chain B: N.131, D.230, E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.445, B:H.447, H2O.3, H2O.6, H2O.6 MG.13: 7 residues within 4Å: Chain B: D.44, W.45, 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:H.447, C:E.490, H2O.7, H2O.9, H2O.9 MG.26: 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.38: 4 residues within 4Å: Chain D: D.230, E.445, H.447, E.490 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.445, D:H.447, H2O.10, H2O.14, H2O.14

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

NA.3: 5 residues within 4Å: Chain A: Y.129, D.230, F.630, N.633 Ligands: GTZ.1 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.591 NA.14: 6 residues within 4Å: Chain B: Y.129, D.230, W.597, F.630, N.633 Ligands: GTZ.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.597, B:N.633 NA.15: 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.27: 6 residues within 4Å: Chain C: Y.129, D.230, W.597, F.630, N.633 Ligands: GTZ.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.630, 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.39: 6 residues within 4Å: Chain D: Y.129, D.230, W.597, F.630, N.633 Ligands: GTZ.37 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.633, D:N.633 NA.40: 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

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

DMS.5: 6 residues within 4Å: Chain A: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.6: 5 residues within 4Å: Chain A: A.63, W.65, D.74, R.339, A.356 Ligand excluded by PLIP DMS.7: 3 residues within 4Å: Chain A: T.300, L.320, R.321 Ligand excluded by PLIP DMS.8: 4 residues within 4Å: Chain A: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.9: 3 residues within 4Å: Chain A: V.113, V.114, H.122 Ligand excluded by PLIP DMS.10: 3 residues within 4Å: Chain A: D.457, P.459 Chain D: Q.474 Ligand excluded by PLIP DMS.16: 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.17: 6 residues within 4Å: Chain B: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.18: 6 residues within 4Å: Chain B: F.62, A.63, W.65, D.74, R.339, A.356 Ligand excluded by PLIP DMS.19: 4 residues within 4Å: Chain B: T.300, L.320, R.321 Ligands: DMS.23 Ligand excluded by PLIP DMS.20: 5 residues within 4Å: Chain B: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.21: 4 residues within 4Å: Chain B: G.304, G.305, V.318, T.319 Ligand excluded by PLIP DMS.22: 3 residues within 4Å: Chain B: V.113, V.114, H.122 Ligand excluded by PLIP DMS.23: 4 residues within 4Å: Chain B: S.298, L.322, N.323 Ligands: DMS.19 Ligand excluded by PLIP DMS.29: 10 residues within 4Å: Chain C: T.258, D.358, V.359, G.360, R.362, R.477, N.478, H.479, P.480, R.511 Ligand excluded by PLIP DMS.30: 5 residues within 4Å: Chain C: R.586, H.651, Q.652, Q.654, Q.657 Ligand excluded by PLIP DMS.31: 6 residues within 4Å: Chain C: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.32: 4 residues within 4Å: Chain C: G.299, T.300, L.320, R.321 Ligand excluded by PLIP DMS.33: 5 residues within 4Å: Chain C: I.605, P.613, W.614, S.615, R.1002 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.36: 4 residues within 4Å: Chain C: Q.79, S.161, W.162, H.245 Ligand excluded by PLIP DMS.41: 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.42: 6 residues within 4Å: Chain D: K.409, N.412, F.413, F.655, Y.671, W.737 Ligand excluded by PLIP DMS.43: 4 residues within 4Å: Chain D: T.300, T.319, L.320, R.321 Ligand excluded by PLIP DMS.44: 4 residues within 4Å: Chain D: E.343, H.345, G.349, L.351 Ligand excluded by PLIP DMS.45: 6 residues within 4Å: Chain D: S.82, L.83, N.84, W.87, L.154, F.156 Ligand excluded by PLIP DMS.46: 5 residues within 4Å: Chain D: I.605, P.613, W.614, S.615, R.1002 Ligand excluded by PLIP DMS.47: 3 residues within 4Å: Chain D: D.74, R.75, L.80 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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