SMTL ID : 3aiw.1 (1 other biounit)

Crystal structure of beta-glucosidase in rye complexed with 2-deoxy-2-fluoroglucoside and dinitrophenol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x DNF: 2,4-DINITROPHENOL(Non-covalent)

DNF.1: 9 residues within 4Å: Chain A: W.191, E.236, T.239, F.243, M.309, W.424, E.507, W.508 Ligands: G2F.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.243 DNF.3: 9 residues within 4Å: Chain B: W.191, E.236, T.239, F.243, M.309, W.424, E.507, W.508 Ligands: G2F.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.243 DNF.5: 9 residues within 4Å: Chain C: W.191, E.236, T.239, F.243, M.309, W.424, E.507, W.508 Ligands: G2F.6 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.243 DNF.7: 9 residues within 4Å: Chain D: W.191, E.236, T.239, F.243, M.309, W.424, E.507, W.508 Ligands: G2F.8 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.243 DNF.9: 9 residues within 4Å: Chain E: W.191, E.236, T.239, F.243, M.309, W.424, E.507, W.508 Ligands: G2F.10 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.243 DNF.11: 9 residues within 4Å: Chain F: W.191, E.236, T.239, F.243, M.309, W.424, E.507, W.508 Ligands: G2F.12 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.243

6 x G2F: 2-deoxy-2-fluoro-alpha-D-glucopyranose(Post Translational Modification)

G2F.2: 12 residues within 4Å: Chain A: Q.88, H.190, N.235, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: DNF.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.88, A:H.190, A:W.508 Water bridges: A:N.505 Halogen bonds: A:N.235 G2F.4: 12 residues within 4Å: Chain B: Q.88, H.190, N.235, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: DNF.3 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.88, B:H.190, B:Y.379, B:W.508 Water bridges: B:N.505 Halogen bonds: B:N.235 G2F.6: 12 residues within 4Å: Chain C: Q.88, H.190, N.235, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: DNF.5 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.88, C:H.190, C:W.508 Water bridges: C:N.505 Halogen bonds: C:N.235 G2F.8: 12 residues within 4Å: Chain D: Q.88, H.190, N.235, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: DNF.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.88, D:H.190, D:Y.379, D:W.508 Water bridges: D:N.505 Halogen bonds: D:N.235 G2F.10: 12 residues within 4Å: Chain E: Q.88, H.190, N.235, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: DNF.9 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.88, E:H.190, E:W.508 Water bridges: E:N.505 Halogen bonds: E:N.235 G2F.12: 12 residues within 4Å: Chain F: Q.88, H.190, N.235, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: DNF.11 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Q.88, F:H.190, F:Y.379, F:W.508 Water bridges: F:N.505 Halogen bonds: F:N.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sue, M. et al., Active-site architecture of benzoxazinone-glucoside beta-D-glucosidases in Triticeae. Plant Sci. (2011)

Release Date

2011-02-23

Peptides

Beta-glucosidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Beta-glucosidase

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