SMTL ID : 6zjq.1

Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB mutant E517Q in complex with galactose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: D.209, W.550, F.583, D.586 Ligands: GAL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.550 NA.2: 4 residues within 4Å: Chain A: F.538, Y.541, P.542, L.544 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.538, A:L.544 NA.3: 1 residues within 4Å: Chain A: D.653 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.653, A:D.653 NA.4: 5 residues within 4Å: Chain A: R.915, P.916, L.956, D.957, A.959 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.916 Water bridges: A:R.915, A:R.915 NA.5: 4 residues within 4Å: Chain A: Q.884, G.894, Q.895, A.897 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.884 NA.34: 5 residues within 4Å: Chain B: D.209, W.550, F.583, D.586 Ligands: GAL.39 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.550 NA.35: 4 residues within 4Å: Chain B: F.538, Y.541, P.542, L.544 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.544, B:L.544 NA.36: 1 residues within 4Å: Chain B: D.653 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.653 NA.37: 5 residues within 4Å: Chain B: R.915, P.916, L.956, D.957, A.959 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.956 Water bridges: B:R.915, B:R.915 NA.38: 4 residues within 4Å: Chain B: Q.884, G.894, Q.895, A.897 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.884

4 x GAL: beta-D-galactopyranose(Non-covalent)

GAL.6: 13 residues within 4Å: Chain A: N.112, D.209, H.370, N.442, E.443, M.483, Y.484, Q.519, H.522, W.550, F.583, D.586 Ligands: NA.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:H.370, A:N.442, A:E.443, A:E.443, A:Q.519 Water bridges: A:N.112, A:N.112, A:N.112, A:D.209, A:D.209, A:D.209 GAL.7: 9 residues within 4Å: Chain A: E.289, K.359, N.362, I.363, N.364, P.608, F.634, W.698, V.705 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.362, A:N.362, A:I.363 Water bridges: A:N.364 Salt bridges: A:K.359 GAL.39: 13 residues within 4Å: Chain B: N.112, D.209, H.370, N.442, E.443, M.483, Y.484, Q.519, H.522, W.550, F.583, D.586 Ligands: NA.34 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.209, B:H.370, B:N.442, B:E.443, B:E.443, B:E.443, B:Y.484, B:Q.519, B:D.586 Water bridges: B:N.112, B:N.112, B:D.209, B:D.209, B:D.209, B:H.397 GAL.40: 9 residues within 4Å: Chain B: E.289, K.359, N.362, I.363, N.364, P.608, F.634, W.698, V.705 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.362, B:N.362, B:I.363 Water bridges: B:E.289, B:N.364 Salt bridges: B:K.359

40 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: P.48, A.49, R.423 Ligand excluded by PLIP ACT.9: 3 residues within 4Å: Chain A: H.339, R.341 Ligands: ACT.15 Ligand excluded by PLIP ACT.10: 4 residues within 4Å: Chain A: R.348, H.374, Q.376, F.377 Ligand excluded by PLIP ACT.11: 7 residues within 4Å: Chain A: D.232, V.233, F.234, E.251, A.252, S.253, R.460 Ligand excluded by PLIP ACT.12: 3 residues within 4Å: Chain A: L.501, N.502, D.503 Ligand excluded by PLIP ACT.13: 3 residues within 4Å: Chain A: V.290, P.291, K.292 Ligand excluded by PLIP ACT.14: 3 residues within 4Å: Chain A: L.70, G.104, H.105 Ligand excluded by PLIP ACT.15: 5 residues within 4Å: Chain A: H.339, R.341, V.350, D.592 Ligands: ACT.9 Ligand excluded by PLIP ACT.16: 7 residues within 4Å: Chain A: T.446, G.447, L.450, A.451, Y.468, D.471, H.476 Ligand excluded by PLIP ACT.17: 3 residues within 4Å: Chain A: R.637, A.701, G.702 Ligand excluded by PLIP ACT.18: 6 residues within 4Å: Chain A: S.923, G.924, F.944, A.945, D.976, H.977 Ligand excluded by PLIP ACT.19: 3 residues within 4Å: Chain A: A.699, D.700, H.703 Ligand excluded by PLIP ACT.20: 5 residues within 4Å: Chain A: K.757, L.760, L.795, H.796, T.797 Ligand excluded by PLIP ACT.21: 3 residues within 4Å: Chain A: A.353, R.356, Q.360 Ligand excluded by PLIP ACT.22: 4 residues within 4Å: Chain A: K.825, Q.826, Y.827, V.855 Ligand excluded by PLIP ACT.23: 2 residues within 4Å: Chain A: A.319, Q.495 Ligand excluded by PLIP ACT.24: 3 residues within 4Å: Chain A: Y.484, G.988, P.989 Ligand excluded by PLIP ACT.25: 2 residues within 4Å: Chain A: K.908, R.922 Ligand excluded by PLIP ACT.26: 2 residues within 4Å: Chain A: D.630, P.656 Ligand excluded by PLIP ACT.27: 5 residues within 4Å: Chain A: R.850, T.853, W.854, E.860, P.999 Ligand excluded by PLIP ACT.41: 3 residues within 4Å: Chain B: P.48, A.49, R.423 Ligand excluded by PLIP ACT.42: 3 residues within 4Å: Chain B: H.339, R.341 Ligands: ACT.48 Ligand excluded by PLIP ACT.43: 4 residues within 4Å: Chain B: R.348, H.374, Q.376, F.377 Ligand excluded by PLIP ACT.44: 7 residues within 4Å: Chain B: D.232, V.233, F.234, E.251, A.252, S.253, R.460 Ligand excluded by PLIP ACT.45: 3 residues within 4Å: Chain B: L.501, N.502, D.503 Ligand excluded by PLIP ACT.46: 3 residues within 4Å: Chain B: V.290, P.291, K.292 Ligand excluded by PLIP ACT.47: 3 residues within 4Å: Chain B: L.70, G.104, H.105 Ligand excluded by PLIP ACT.48: 5 residues within 4Å: Chain B: H.339, R.341, V.350, D.592 Ligands: ACT.42 Ligand excluded by PLIP ACT.49: 7 residues within 4Å: Chain B: T.446, G.447, L.450, A.451, Y.468, D.471, H.476 Ligand excluded by PLIP ACT.50: 3 residues within 4Å: Chain B: R.637, A.701, G.702 Ligand excluded by PLIP ACT.51: 6 residues within 4Å: Chain B: S.923, G.924, F.944, A.945, D.976, H.977 Ligand excluded by PLIP ACT.52: 3 residues within 4Å: Chain B: A.699, D.700, H.703 Ligand excluded by PLIP ACT.53: 5 residues within 4Å: Chain B: K.757, L.760, L.795, H.796, T.797 Ligand excluded by PLIP ACT.54: 3 residues within 4Å: Chain B: A.353, R.356, Q.360 Ligand excluded by PLIP ACT.55: 4 residues within 4Å: Chain B: K.825, Q.826, Y.827, V.855 Ligand excluded by PLIP ACT.56: 2 residues within 4Å: Chain B: A.319, Q.495 Ligand excluded by PLIP ACT.57: 3 residues within 4Å: Chain B: Y.484, G.988, P.989 Ligand excluded by PLIP ACT.58: 2 residues within 4Å: Chain B: K.908, R.922 Ligand excluded by PLIP ACT.59: 2 residues within 4Å: Chain B: D.630, P.656 Ligand excluded by PLIP ACT.60: 5 residues within 4Å: Chain B: R.850, T.853, W.854, E.860, P.999 Ligand excluded by PLIP

12 x MLI: MALONATE ION(Non-functional Binders)

MLI.28: 6 residues within 4Å: Chain A: R.341, T.558, H.567, Y.568, D.592, R.594 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.341, A:D.592 Salt bridges: A:R.594 MLI.29: 5 residues within 4Å: Chain A: H.977, R.1000, D.1001, A.1002, D.1003 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.1003, A:D.1003 Salt bridges: A:H.977, A:R.1000 MLI.30: 4 residues within 4Å: Chain A: R.798, L.800, R.817 Chain B: H.123 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.798 Salt bridges: A:R.798, A:R.817, B:H.123 MLI.31: 5 residues within 4Å: Chain A: V.262, R.264, S.299, A.300, A.301 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.264 MLI.32: 8 residues within 4Å: Chain A: I.314, A.315, I.316, K.458, P.462, R.464, P.465, D.478 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.316, A:P.462 Salt bridges: A:K.458 MLI.33: 5 residues within 4Å: Chain A: N.163, E.186, E.189, N.190, T.191 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.186 MLI.61: 6 residues within 4Å: Chain B: R.341, T.558, H.567, Y.568, D.592, R.594 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.341, B:D.592 Salt bridges: B:R.594 MLI.62: 5 residues within 4Å: Chain B: H.977, R.1000, D.1001, A.1002, D.1003 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.1003 Salt bridges: B:H.977, B:R.1000 MLI.63: 4 residues within 4Å: Chain A: H.123 Chain B: R.798, L.800, R.817 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.798 Salt bridges: B:R.798, B:R.817, A:H.123 MLI.64: 5 residues within 4Å: Chain B: V.262, R.264, S.299, A.300, A.301 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.264 MLI.65: 8 residues within 4Å: Chain B: I.314, A.315, I.316, K.458, P.462, R.464, P.465, D.478 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.316, B:P.462 Salt bridges: B:K.458 MLI.66: 5 residues within 4Å: Chain B: N.163, E.186, E.189, N.190, T.191 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.186, B:T.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutkiewicz, M. et al., Mapping the Transglycosylation Relevant Sites of Cold-Adapted beta-d-Galactosidase fromArthrobactersp. 32cB. Int J Mol Sci (2020)

Release Date

2020-08-05

Peptides

Beta-galactosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-galactosidase

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