SMTL ID : 4i3g.1 (1 other biounit)

Crystal Structure of DesR, a beta-glucosidase from Streptomyces venezuelae in complex with D-glucose.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 13 residues within 4Å: Chain A: V.81, D.99, R.105, L.149, R.163, K.196, H.197, R.207, M.239, Y.242, D.274, S.411, E.579 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.105, A:R.163, A:R.163, A:K.196, A:H.197, A:H.197, A:R.207, A:Y.242, A:Y.242, A:S.411 Water bridges: A:K.196, A:R.207 Salt bridges: A:R.207

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

SO4.2: 3 residues within 4Å: Chain A: Q.109, R.357, K.359 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.109 Water bridges: A:T.110, A:K.359 Salt bridges: A:R.357, A:K.359 SO4.3: 2 residues within 4Å: Chain A: R.378, S.622 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.378 Salt bridges: A:R.378 SO4.4: 5 residues within 4Å: Chain A: G.590, T.591, Q.592, D.593, K.594 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.593, A:K.594 Water bridges: A:Q.592, A:Q.592, A:K.594, A:K.594 Salt bridges: A:K.594 SO4.5: 4 residues within 4Å: Chain A: D.125, D.126, T.127, R.177 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.125, A:D.125, A:D.126, A:T.127 Water bridges: A:D.126, A:R.177, A:R.177, A:R.177, A:T.771, A:K.772 Salt bridges: A:R.177 SO4.6: 3 residues within 4Å: Chain A: A.662, E.663, N.664 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.663, A:N.664, A:N.664 SO4.7: 3 residues within 4Å: Chain A: G.381, Q.382, R.625 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.605, A:N.605 Salt bridges: A:R.625 SO4.8: 4 residues within 4Å: Chain A: D.696, K.764, K.765, S.817 7 PLIP interactions: 7 interactions with chain A Water bridges: A:D.696, A:K.764, A:Q.812, A:S.817, A:S.817 Salt bridges: A:K.764, A:K.765 SO4.9: 2 residues within 4Å: Chain A: T.735, R.737 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.716, A:R.737, A:R.737 Salt bridges: A:R.737

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.10: 4 residues within 4Å: Chain A: F.208, Y.242, W.275, L.276 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.208 pi-Cation interactions: A:F.208

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

EDO.11: 3 residues within 4Å: Chain A: R.789, Q.793, T.804 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.789, A:Q.793, A:T.804 Water bridges: A:T.804 EDO.12: 3 residues within 4Å: Chain A: T.727, D.788, R.789 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.789 Water bridges: A:G.729, A:R.790

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zmudka, M.W. et al., The structure of DesR from Streptomyces venezuelae, a beta-glucosidase involved in macrolide activation. Protein Sci. (2013)

Release Date

2013-02-20

Peptides

Beta-glucosidase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-glucosidase

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