SMTL ID : 3air.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

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

G2F.1: 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.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.88, A:H.190, A:W.508 Water bridges: A:N.505 G2F.3: 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.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.88, B:H.190, B:Y.379, B:W.508 Water bridges: B:N.505 G2F.5: 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.6 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.88, C:H.190, C:W.508 Water bridges: C:N.505 G2F.7: 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.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.88, D:H.190, D:Y.379, D:W.508 Water bridges: D:N.505 G2F.9: 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.10 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:Q.88, E:H.190, E:W.508 Water bridges: E:N.505 G2F.11: 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.12 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.88, F:H.190, F:Y.379, F:W.508 Water bridges: F:N.505

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

DNF.2: 10 residues within 4Å: Chain A: W.191, E.236, T.239, F.243, H.250, M.309, W.424, E.507, W.508 Ligands: G2F.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:T.239, A:F.243, A:W.424, A:W.424 Water bridges: A:H.250 DNF.4: 10 residues within 4Å: Chain B: W.191, E.236, T.239, F.243, H.250, M.309, W.424, E.507, W.508 Ligands: G2F.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.239, B:F.243, B:W.424, B:W.424 Water bridges: B:H.250 DNF.6: 10 residues within 4Å: Chain C: W.191, E.236, T.239, F.243, H.250, M.309, W.424, E.507, W.508 Ligands: G2F.5 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.239, C:F.243, C:W.424, C:W.424 Water bridges: C:H.250 DNF.8: 10 residues within 4Å: Chain D: W.191, E.236, T.239, F.243, H.250, M.309, W.424, E.507, W.508 Ligands: G2F.7 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.239, D:F.243, D:W.424, D:W.424 Water bridges: D:H.250 DNF.10: 10 residues within 4Å: Chain E: W.191, E.236, T.239, F.243, H.250, M.309, W.424, E.507, W.508 Ligands: G2F.9 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:T.239, E:F.243, E:W.424, E:W.424 Water bridges: E:H.250 DNF.12: 10 residues within 4Å: Chain F: W.191, E.236, T.239, F.243, H.250, M.309, W.424, E.507, W.508 Ligands: G2F.11 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:T.239, F:F.243, F:W.424, F:W.424 Water bridges: F:H.250

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

2011-03-16

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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