SMTL ID : 3thd.2 (1 other biounit)

Crystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-dimer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: T.439, N.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.441 Water bridges: A:N.441 NAG.2: 4 residues within 4Å: Chain A: Y.379, S.474, N.475, I.482 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.475 Water bridges: A:Y.379, A:N.475, A:N.475, A:N.475 NAG.3: 6 residues within 4Å: Chain A: E.357, H.500, W.504, N.532, P.590, T.592 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.532 Water bridges: A:W.504 NAG.4: 3 residues within 4Å: Chain A: N.224, T.226, D.227 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.224 NAG.11: 2 residues within 4Å: Chain B: T.439, N.441 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.439 Water bridges: B:N.441, B:N.441 NAG.12: 5 residues within 4Å: Chain B: Y.379, V.473, S.474, N.475, I.482 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.475 NAG.13: 2 residues within 4Å: Chain B: T.355, N.532 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.355, B:N.532 Water bridges: B:E.357, B:N.532, B:N.532, B:N.532, B:N.532 NAG.14: 2 residues within 4Å: Chain B: N.224, D.227 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.224 Water bridges: B:D.227, B:D.227

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: S.31, H.33, Q.58, T.59, R.98 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: S.31, H.33, Q.58, T.59, R.98 Ligand excluded by PLIP

2 x DGJ: (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol(Non-covalent)

DGJ.6: 14 residues within 4Å: Chain A: Y.60, I.103, C.104, A.105, E.106, N.164, E.165, E.245, Y.247, W.250, L.251, Y.283, Y.308, Y.310 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.60, A:A.105, A:E.106, A:N.164, A:E.165, A:Y.247, A:Y.283 DGJ.16: 14 residues within 4Å: Chain B: Y.60, I.103, C.104, A.105, E.106, N.164, E.165, E.245, Y.247, W.250, L.251, Y.283, Y.308, Y.310 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.60, B:Y.60, B:A.105, B:E.106, B:N.164, B:E.165, B:Y.247, B:Y.247, B:Y.310

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 2 residues within 4Å: Chain A: R.328, Q.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.332 Salt bridges: A:R.328 SO4.8: 5 residues within 4Å: Chain A: S.299, P.300, Y.301, R.434, N.435 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.301, A:N.435 Water bridges: A:S.299, A:N.414, A:R.434, A:R.434 Salt bridges: A:R.434 SO4.17: 2 residues within 4Å: Chain B: R.328, Q.332 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.332 Salt bridges: B:R.328 SO4.18: 5 residues within 4Å: Chain B: S.299, P.300, Y.301, R.434, N.435 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.301, B:N.435 Water bridges: B:R.434, B:D.468 Salt bridges: B:R.434

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

EDO.9: 6 residues within 4Å: Chain A: F.219, G.220, T.221, G.222, S.223, Y.247 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.220, A:G.222 EDO.10: 4 residues within 4Å: Chain A: A.292, Y.293, W.294, Y.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.293, A:Y.293 EDO.19: 5 residues within 4Å: Chain B: F.219, G.220, T.221, G.222, S.223 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.220, B:G.222 EDO.20: 4 residues within 4Å: Chain B: A.292, Y.293, W.294, Y.390 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.293, B:Y.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Crystal structure of human beta-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases. J.Biol.Chem. (2012)

Release Date

2011-12-07

Peptides

Beta-galactosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Beta-galactosidase

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