SMTL ID : 1v03.1

Crystal structure of the Sorghum bicolor dhurrinase 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

BGC.1: 14 residues within 4Å: Chain A: Q.90, H.194, W.195, N.239, D.240, Y.382, W.427, E.455, W.504, E.511, W.512, F.520 Ligands: CCN.2, IPH.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.90, A:H.194, A:H.194, A:N.239, A:W.512 Water bridges: A:W.427, A:N.509, A:E.511 BGC.4: 14 residues within 4Å: Chain B: Q.90, H.194, W.195, N.239, D.240, Y.382, W.427, E.455, W.504, E.511, W.512, F.520 Ligands: CCN.5, IPH.6 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Q.90, B:H.194, B:H.194, B:N.239, B:W.512 Water bridges: B:W.427, B:N.509, B:E.511

2 x CCN: ACETONITRILE(Non-functional Binders)

CCN.2: 4 residues within 4Å: Chain A: T.243, W.427 Ligands: BGC.1, IPH.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.427 Water bridges: A:N.310 CCN.5: 4 residues within 4Å: Chain B: T.243, W.427 Ligands: BGC.4, IPH.6 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.427 Hydrogen bonds: B:T.243 Water bridges: B:N.310

2 x IPH: PHENOL(Non-covalent)

IPH.3: 6 residues within 4Å: Chain A: T.243, V.247, L.254, E.511 Ligands: BGC.1, CCN.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.243 IPH.6: 6 residues within 4Å: Chain B: T.243, V.247, L.254, E.511 Ligands: BGC.4, CCN.5 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:T.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Verdoucq, L. et al., Structural Determinants of Substrate Specificity in Family 1 Beta-Glucosidases: Novel Insights from the Crystal Structure of Sorghum Dhurrinase-1, a Plant Beta-Glucosidase with Strict Specificity, in Complex with its Natural Substrate. J.Biol.Chem. (2004)

Release Date

2004-05-20

Peptides

DHURRINASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DHURRINASE