SMTL ID : 2dga.1

Crystal structure of hexameric beta-glucosidase in wheat

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-hexamer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: Q.315, D.316, S.411 Chain F: T.61, R.479 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:Q.315, A:D.316, A:S.411, A:S.411 Water bridges: A:D.316, F:Q.67, F:R.479 Salt bridges: F:R.479 SO4.5: 5 residues within 4Å: Chain B: Q.315, D.316, S.411 Chain E: T.61, R.479 10 PLIP interactions: 3 interactions with chain E, 7 interactions with chain B Water bridges: E:Q.67, E:R.479, B:D.316, B:D.316, B:D.316 Salt bridges: E:R.479 Hydrogen bonds: B:Q.315, B:D.316, B:S.411, B:S.411 SO4.9: 5 residues within 4Å: Chain C: Q.315, D.316, S.411 Chain D: T.61, R.479 10 PLIP interactions: 7 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:Q.315, C:D.316, C:S.411, C:S.411 Water bridges: C:D.316, C:D.316, C:D.316, D:Q.67, D:R.479 Salt bridges: D:R.479 SO4.13: 5 residues within 4Å: Chain C: T.61, R.479 Chain D: Q.315, D.316, S.411 10 PLIP interactions: 3 interactions with chain C, 7 interactions with chain D Water bridges: C:Q.67, C:R.479, D:D.316, D:D.316, D:D.316 Salt bridges: C:R.479 Hydrogen bonds: D:Q.315, D:D.316, D:S.411, D:S.411 SO4.17: 5 residues within 4Å: Chain B: T.61, R.479 Chain E: Q.315, D.316, S.411 8 PLIP interactions: 5 interactions with chain E, 3 interactions with chain B Hydrogen bonds: E:Q.315, E:D.316, E:S.411, E:S.411 Water bridges: E:D.316, B:Q.67, B:R.479 Salt bridges: B:R.479 SO4.21: 5 residues within 4Å: Chain A: T.61, R.479 Chain F: Q.315, D.316, S.411 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain A Hydrogen bonds: F:Q.315, F:D.316, F:S.411, F:S.411 Water bridges: F:D.316, A:Q.67, A:R.479 Salt bridges: A:R.479

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: E.236, T.239, D.307, N.377, Y.379, W.424 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 10 residues within 4Å: Chain A: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 5 residues within 4Å: Chain A: H.250, E.507, W.508, S.509, L.510 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain B: E.236, T.239, D.307, N.377, Y.379, W.424 Ligands: GOL.7 Ligand excluded by PLIP GOL.7: 10 residues within 4Å: Chain B: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: GOL.6 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain B: H.250, E.507, W.508, S.509, L.510 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain C: E.236, T.239, D.307, N.377, Y.379, W.424 Ligands: GOL.11 Ligand excluded by PLIP GOL.11: 10 residues within 4Å: Chain C: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: GOL.10 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain C: H.250, E.507, W.508, S.509, L.510 Ligand excluded by PLIP GOL.14: 7 residues within 4Å: Chain D: E.236, T.239, D.307, N.377, Y.379, W.424 Ligands: GOL.15 Ligand excluded by PLIP GOL.15: 10 residues within 4Å: Chain D: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: GOL.14 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain D: H.250, E.507, W.508, S.509, L.510 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain E: E.236, T.239, D.307, N.377, Y.379, W.424 Ligands: GOL.19 Ligand excluded by PLIP GOL.19: 10 residues within 4Å: Chain E: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: GOL.18 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain E: H.250, E.507, W.508, S.509, L.510 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain F: E.236, T.239, D.307, N.377, Y.379, W.424 Ligands: GOL.23 Ligand excluded by PLIP GOL.23: 10 residues within 4Å: Chain F: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508, F.516 Ligands: GOL.22 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain F: H.250, E.507, W.508, S.509, L.510 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sue, M. et al., Molecular and Structural Characterization of Hexameric beta-D-Glucosidases in Wheat and Rye. Plant Physiol. (2006)

Release Date

2006-07-04

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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