SMTL ID : 3vkk.1

Crystal Structure Of The Covalent Intermediate Of Human Cytosolic Beta-Glucosidase-mannose complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: D.175, L.176, G.187, G.325, I.326, L.327, Q.328 Ligands: OLA.6 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 GOL.3: 1 residues within 4Å: Chain A: G.90 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.89, A:G.90 GOL.7: 4 residues within 4Å: Chain A: H.185, T.188, G.189, Q.192 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.188, A:T.188 Water bridges: A:Q.192

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

CL.2: 5 residues within 4Å: Chain A: A.15, S.77, L.78, H.120, D.122 Ligand excluded by PLIP CL.4: 5 residues within 4Å: Chain A: F.225, A.226, V.227, Q.307, W.345 Ligand excluded by PLIP

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.5: 13 residues within 4Å: Chain A: N.167, S.170, V.171, L.176, M.178, G.190, Y.191, A.194, F.225, F.249, H.250, L.253 Ligands: OLA.6 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.171, A:V.171, A:L.176, A:Y.191, A:A.194, A:F.225, A:H.250, A:L.253

1 x OLA: OLEIC ACID(Non-covalent)

OLA.6: 11 residues within 4Å: Chain A: V.171, V.227, A.246, H.250, R.312, I.326, L.327, F.334, W.345 Ligands: GOL.1, PLM.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.171, A:V.227, A:A.246, A:H.250, A:I.326, A:L.327, A:F.334, A:F.334, A:W.345

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.8: 10 residues within 4Å: Chain A: Q.17, H.120, Q.165, F.225, Q.307, Y.309, E.373, W.417, E.424, W.425 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.17, A:Q.17, A:H.120, A:Q.165, A:Y.309, A:E.424 Water bridges: A:N.422

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 7 residues within 4Å: Chain A: R.75, N.164, Q.165, S.223, Q.307, T.372, E.373 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noguchi, J. et al., Structural basis for inhibition mechanism of human cytosolic beta-glucosidase by monnoside. To be Published

Release Date

2012-11-21

Peptides

Cytosolic beta-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytosolic beta-glucosidase

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