SMTL ID : 3wq6.2 (1 other biounit)

beta-Primeverosidase in complex with disaccharide substrate-analog N-beta-primeverosylamidine, artificial aglycone derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x ZPA: 4-(N-benzylsuccinimide-3-sulfanyl)-N-(6-O-beta-D-xylopyranosyl-beta-D-glucopyranosyl)butylamidine(Non-covalent)

ZPA.1: 22 residues within 4Å: Chain A: Q.53, H.157, W.158, N.202, E.203, W.205, S.206, Y.209, L.217, V.273, Y.275, Y.345, V.386, F.389, E.416, W.463, E.470, W.471, L.472, S.473, Q.477, F.479 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:W.158, A:W.205, A:V.273, A:Y.275, A:Y.345, A:F.389, A:L.472 Hydrogen bonds: A:Q.53, A:Q.53, A:H.157, A:N.202, A:E.203, A:E.203, A:N.343, A:E.470, A:S.473, A:S.473, A:S.473, A:Q.477 Water bridges: A:Y.209

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

NAG.2: 4 residues within 4Å: Chain A: S.33, N.35, T.37, L.506 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.506 Hydrogen bonds: A:N.35 Water bridges: A:N.35, A:S.38 NAG.3: 2 residues within 4Å: Chain A: N.422, N.424 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.422, A:N.424 Water bridges: A:N.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saino, H. et al., Crystal structures of beta-primeverosidase in complex with disaccharide amidine inhibitors. J.Biol.Chem. (2014)

Release Date

2014-04-23

Peptides

beta-primeverosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

beta-primeverosidase

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