SMTL ID : 3wf0.1 (1 other biounit)

Crystal structure of human beta-galactosidase in complex with 6S-NBI-DGJ

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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.463, N.465 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.465 NAG.2: 6 residues within 4Å: Chain A: Y.403, P.404, V.497, S.498, N.499, I.506 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.499 Water bridges: A:N.499 NAG.3: 4 residues within 4Å: Chain A: W.528, N.556, P.614, T.616 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.556 NAG.4: 3 residues within 4Å: Chain A: N.248, T.250, D.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.248 NAG.11: 1 residues within 4Å: Chain B: N.465 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.465 NAG.12: 5 residues within 4Å: Chain B: Y.403, V.497, S.498, N.499, I.506 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.499 NAG.13: 1 residues within 4Å: Chain B: N.556 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.556 NAG.14: 3 residues within 4Å: Chain B: N.248, T.250, D.251 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.248 Water bridges: B:N.248, B:T.250

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

CL.5: 5 residues within 4Å: Chain A: S.55, H.57, Q.82, T.83, R.122 Ligand excluded by PLIP CL.15: 5 residues within 4Å: Chain B: S.55, H.57, Q.82, T.83, R.122 Ligand excluded by PLIP

2 x 6DJ: (3Z,6S,7R,8S,8aS)-3-(butylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-6,7,8-triol(Non-covalent)

6DJ.6: 14 residues within 4Å: Chain A: Y.84, I.127, C.128, A.129, E.130, N.188, E.189, E.269, Y.271, W.274, L.275, Y.307, Y.334, Y.486 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.486 Hydrogen bonds: A:Y.84, A:Y.84, A:A.129, A:E.130, A:N.188, A:Y.307 6DJ.16: 14 residues within 4Å: Chain B: Y.84, I.127, C.128, A.129, E.130, N.188, E.189, E.269, Y.271, W.274, L.275, Y.307, Y.334, Y.486 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.84, B:Y.84, B:A.129, B:E.130, B:N.188, B:N.188 Water bridges: B:E.130

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

SO4.7: 2 residues within 4Å: Chain A: R.352, Q.356 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.356, A:Q.356 Salt bridges: A:R.352 SO4.8: 5 residues within 4Å: Chain A: S.323, P.324, Y.325, R.458, N.459 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.325, A:N.459 Water bridges: A:R.458 Salt bridges: A:R.458 SO4.17: 2 residues within 4Å: Chain B: R.352, Q.356 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.356 Salt bridges: B:R.352 SO4.18: 5 residues within 4Å: Chain B: S.323, P.324, Y.325, R.458, N.459 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.325, B:N.459 Water bridges: B:R.458, B:R.458, B:R.458, B:D.492 Salt bridges: B:R.458

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

EDO.9: 4 residues within 4Å: Chain A: G.244, G.246, S.247, Y.271 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.244, A:G.246, A:S.247, A:S.247 EDO.10: 4 residues within 4Å: Chain A: A.316, Y.317, W.318, Y.414 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.317, A:Y.317 EDO.19: 5 residues within 4Å: Chain B: F.243, G.244, T.245, G.246, S.247 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.244, B:G.246, B:S.247 Water bridges: B:D.242, B:D.242 EDO.20: 4 residues within 4Å: Chain B: A.316, Y.317, W.318, Y.414 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.317, B:Y.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Suzuki, H. et al., Structural basis of pharmacological chaperoning for human beta-galactosidase. to be published

Release Date

2014-04-23

Peptides

Beta-galactosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Beta-galactosidase

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