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

Crystal structure of human beta-galactosidase in complex with NOEV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.11 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: 5 residues within 4Å: Chain A: Y.403, P.404, S.498, N.499, I.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.499 NAG.3: 3 residues within 4Å: Chain A: W.528, N.556, 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 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: T.463, N.465 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.465 NAG.12: 6 residues within 4Å: Chain B: Y.403, P.404, V.497, S.498, N.499, I.506 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.499 NAG.13: 3 residues within 4Å: Chain B: E.381, G.555, N.556 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.381 Water bridges: B:T.379, B:E.381, B:N.556, B:N.556 NAG.14: 3 residues within 4Å: Chain B: N.248, T.250, D.251 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.248

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

CL.5: 6 residues within 4Å: Chain A: S.55, H.57, Q.82, T.83, R.122, Y.307 Ligand excluded by PLIP CL.15: 6 residues within 4Å: Chain B: S.55, H.57, Q.82, T.83, Y.84, R.122 Ligand excluded by PLIP

2 x N8V: (1S,2S,3S,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol(Non-covalent)

N8V.6: 17 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, H.277, Y.307, N.322, Y.332, Y.334, Y.486 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.271, A:N.322, A:Y.486 Hydrogen bonds: A:Y.84, A:Y.84, A:A.129, A:E.130, A:N.188, A:E.189 Water bridges: A:Y.271 N8V.16: 17 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, H.277, Y.307, N.322, Y.332, Y.334, Y.486 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:Y.271, B:N.322, B:Y.486, B:Y.486 Hydrogen bonds: B:Y.84, B:Y.84, B:Y.84, B:A.129, B:E.130, B:N.188, B:E.189, B:Y.332, B:Y.334, B:Y.334

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

SO4.7: 2 residues within 4Å: Chain A: R.352, Q.356 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.323, A:Y.325, A:N.459 Water bridges: A:R.458 Salt bridges: A:R.458 SO4.17: 3 residues within 4Å: Chain B: R.352, N.353, Q.356 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.353, B:Q.356 Salt bridges: B:R.352 SO4.18: 6 residues within 4Å: Chain B: S.323, P.324, Y.325, R.458, N.459, Y.489 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.325, B:N.459 Water bridges: B:R.458 Salt bridges: B:R.458

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

EDO.9: 5 residues within 4Å: Chain A: F.243, G.244, T.245, G.246, S.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.244, A:G.246, A:S.247 Water bridges: 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 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.244, B:G.246, B:S.247, B:S.247 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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