SMTL ID : 5z5i.1

Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08 in complex with L-arabinose and D-xylose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: D.316, S.344, D.503 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.316, A:S.344, A:D.503, A:D.503, H2O.14 CA.6: 3 residues within 4Å: Chain B: D.316, S.344, D.503 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.316, B:S.344, B:D.503, B:D.503, H2O.34

2 x FUB: beta-L-arabinofuranose(Non-covalent)

FUB.2: 12 residues within 4Å: Chain A: D.14, F.31, F.73, A.74, I.120, D.121, E.177, T.197, H.238, H.254, R.269 Ligands: XYS.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.74, A:D.121, A:T.197, A:R.269, A:R.269 Salt bridges: A:H.238, A:H.254, A:R.269 FUB.7: 12 residues within 4Å: Chain B: D.14, F.31, F.73, A.74, I.120, D.121, E.177, T.197, H.238, H.254, R.269 Ligands: XYS.8 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:A.74, B:D.121, B:T.197, B:T.197, B:H.238, B:R.269, B:R.269 Water bridges: B:E.177, B:E.177 Salt bridges: B:H.238, B:H.254, B:R.269

2 x XYS: alpha-D-xylopyranose(Non-covalent)

XYS.3: 9 residues within 4Å: Chain A: I.120, Y.175, E.177, G.196, T.197, E.198, F.480 Chain B: Y.261 Ligands: FUB.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.177, A:T.197, A:E.198 Water bridges: A:Y.175, A:Y.175, A:E.198, A:E.198 XYS.8: 9 residues within 4Å: Chain A: Y.261 Chain B: I.120, Y.175, E.177, G.196, T.197, E.198, F.480 Ligands: FUB.7 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.177, B:T.197, B:E.198 Water bridges: B:Y.175, B:Y.175, B:E.198, B:E.198

4 x XYP: beta-D-xylopyranose(Non-covalent)

XYP.4: 5 residues within 4Å: Chain A: R.57, E.107, W.108, S.109, E.110 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.57, A:E.110 Water bridges: A:R.57, A:R.57, A:E.107, A:E.107, A:E.107, A:E.110 XYP.5: 5 residues within 4Å: Chain A: R.19, Q.243, Y.244, H.245, G.247 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.19, A:H.245 Water bridges: A:H.245, A:D.246 Salt bridges: A:R.19 XYP.9: 5 residues within 4Å: Chain B: R.57, E.107, W.108, S.109, E.110 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.57, B:E.110 Water bridges: B:R.57, B:R.57, B:E.107, B:E.107, B:E.107 XYP.10: 5 residues within 4Å: Chain B: R.19, Q.243, Y.244, H.245, G.247 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.19, B:H.245 Water bridges: B:H.245, B:D.246 Salt bridges: B:R.19

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rohman, A. et al., Structural basis of product inhibition by arabinose and xylose of the thermostable GH43 beta-1,4-xylosidase from Geobacillus thermoleovorans IT-08. PLoS ONE (2018)

Release Date

2018-04-25

Peptides

Beta-xylosidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Beta-xylosidase

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