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

Crystal structure of beta-glucosidase in rye

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 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 F, 3 interactions with chain A Water bridges: F:K.62, F:Q.67, F:R.479, F:R.479 Salt bridges: F:R.479 Hydrogen bonds: A:D.316, A:S.411, A:S.411 SO4.3: 5 residues within 4Å: Chain B: Q.315, D.316, S.411 Chain E: T.61, R.479 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain E Hydrogen bonds: B:D.316, B:S.411, B:S.411 Water bridges: B:D.316, B:D.316, E:K.62, E:Q.67, E:R.479, E:R.479 Salt bridges: E:R.479 SO4.5: 5 residues within 4Å: Chain C: Q.315, D.316, S.411 Chain D: T.61, R.479 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Water bridges: D:K.62, D:Q.67, D:R.479, D:R.479, C:D.316, C:D.316 Salt bridges: D:R.479 Hydrogen bonds: C:D.316, C:S.411, C:S.411 SO4.7: 5 residues within 4Å: Chain C: T.61, R.479 Chain D: Q.315, D.316, S.411 10 PLIP interactions: 5 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:D.316, D:S.411, D:S.411 Water bridges: D:D.316, D:D.316, C:K.62, C:Q.67, C:R.479, C:R.479 Salt bridges: C:R.479 SO4.9: 5 residues within 4Å: Chain B: T.61, R.479 Chain E: Q.315, D.316, S.411 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain B Hydrogen bonds: E:D.316, E:S.411, E:S.411 Water bridges: B:K.62, B:Q.67, B:R.479, B:R.479 Salt bridges: B:R.479 SO4.11: 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 A, 3 interactions with chain F Water bridges: A:K.62, A:Q.67, A:R.479, A:R.479 Salt bridges: A:R.479 Hydrogen bonds: F:D.316, F:S.411, F:S.411

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.88, A:Q.88, A:E.236, A:E.507 Water bridges: A:N.377 GOL.4: 8 residues within 4Å: Chain B: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.88, B:Q.88, B:E.236, B:Y.379, B:E.507 Water bridges: B:N.377 GOL.6: 8 residues within 4Å: Chain C: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.88, C:Q.88, C:E.236, C:E.507 Water bridges: C:N.377 GOL.8: 8 residues within 4Å: Chain D: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Q.88, D:Q.88, D:E.236, D:Y.379, D:E.507 Water bridges: D:N.377 GOL.10: 8 residues within 4Å: Chain E: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.88, E:Q.88, E:E.236, E:E.507 Water bridges: E:N.377 GOL.12: 8 residues within 4Å: Chain F: Q.88, E.236, Y.379, W.424, E.452, W.500, E.507, W.508 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:Q.88, F:Q.88, F:E.236, F:Y.379, F:E.507 Water bridges: F:N.377

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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