SMTL ID : 5dmy.1

Beta-galactosidase - construct 33-930

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: N.649, D.650, V.652, H.653, D.681 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.649, A:V.652, A:D.681, H2O.13, H2O.27, H2O.28 MG.2: 2 residues within 4Å: Chain A: Q.336, Q.351 No protein-ligand interaction detected (PLIP) MG.7: 5 residues within 4Å: Chain B: E.85, E.87, N.398, N.400, T.612 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.85, B:E.87, B:N.398, B:T.612, H2O.45 MG.8: 4 residues within 4Å: Chain B: N.649, V.652, H.653, D.681 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:N.649, B:V.652, B:D.681, H2O.52, H2O.56 MG.9: 5 residues within 4Å: Chain C: E.85, E.87, N.398, N.400, T.612 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.85, C:E.87, C:N.398, H2O.66, H2O.76

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

NA.3: 4 residues within 4Å: Chain A: A.543, N.545, D.568, T.640 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.545, A:D.568, A:T.640 NA.10: 3 residues within 4Å: Chain C: N.649, V.652, D.681 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.652, C:D.681 NA.11: 4 residues within 4Å: Chain C: D.335, G.337, D.601, Y.602 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:G.337, C:Q.351, C:D.601

1 x NI: NICKEL (II) ION(Non-covalent)

NI.4: 5 residues within 4Å: Chain A: E.85, E.87, N.398, N.400, T.612 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.85, A:E.87, A:N.398, A:T.612, H2O.8

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 7 residues within 4Å: Chain A: I.76, Q.78, Y.80, L.91, S.838, Y.839, Q.840 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.78, A:Y.839, A:Q.840 EDO.6: 8 residues within 4Å: Chain A: Y.550, D.639, H.656, I.657, P.659, A.660, N.765, V.768 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.550, A:I.657, A:N.765 Water bridges: A:Y.550, A:Y.550

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lazidou, A. et al., Rational protein engineering toward the development of a beta-galactosidase with improved functional properties. To Be Published

Release Date

2016-10-05

Peptides

Beta-galactosidase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Beta-galactosidase