SMTL ID : 2zox.1

Crystal Structure of the Covalent Intermediate of Human Cytosolic beta-Glucosidase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x GLC: alpha-D-glucopyranose(Post Translational Modification)

GLC.1: 11 residues within 4Å: Chain A: Q.17, H.120, N.164, Q.165, Y.309, W.345, E.373, W.417, E.424, W.425, F.433 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.17, A:H.120, A:N.164, A:Y.309, A:E.373, A:E.424, A:W.425 Water bridges: A:Q.165, A:Q.165, A:N.422

1 x PNG: 4-nitrophenyl alpha-D-glucopyranoside(Non-covalent)

PNG.2: 10 residues within 4Å: Chain A: S.274, M.275, K.278, Q.279, E.318, N.319, K.320, K.321, G.322, E.331 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.278, A:K.278 Hydrogen bonds: A:S.274, A:E.318, A:G.322 Salt bridges: A:K.278

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: R.75, N.164, S.223, Q.307, T.372 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: T.188, Q.192, R.285 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.188, A:R.285, H2O.5

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 7 residues within 4Å: Chain A: M.172, F.179, E.424, W.425, N.426, Q.427 Ligands: PLM.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.426, A:N.426, A:Q.427 Water bridges: A:W.345, A:E.424

2 x PLM: PALMITIC ACID(Non-covalent)

PLM.6: 15 residues within 4Å: Chain A: N.167, V.168, S.170, V.171, G.190, Y.191, F.225, F.249, H.250, L.253, F.254, I.326, W.345 Ligands: PO4.5, OLA.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:N.167, A:V.168, A:V.171, A:Y.191, A:F.225, A:F.225, A:H.250, A:L.253, A:F.254, A:I.326, A:W.345 PLM.8: 5 residues within 4Å: Chain A: Q.279, G.280, Y.281, G.322, L.324 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.281

1 x OLA: OLEIC ACID(Non-covalent)

OLA.7: 13 residues within 4Å: Chain A: V.171, V.227, A.246, F.249, H.250, R.312, I.326, L.327, I.332, F.334, W.345 Ligands: PLM.6, GOL.9 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.227, A:A.246, A:F.249, A:H.250, A:I.326, A:L.327, A:I.332, A:F.334, A:F.334, A:W.345, A:W.345

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 9 residues within 4Å: Chain A: D.175, L.176, F.186, G.187, G.325, I.326, L.327, Q.328 Ligands: OLA.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.175, A:G.187, A:I.326, A:L.327, A:Q.328

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noguchi, J. et al., Crystal structure of the covalent intermediate of human cytosolic beta-glucosidase. Biochem.Biophys.Res.Commun. (2008)

Release Date

2008-09-30

Peptides

Cytosolic beta-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytosolic beta-glucosidase

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