SMTL ID : 5z5d.1

Crystal structure of a thermostable glycoside hydrolase family 43 {beta}-1,4-xylosidase from Geobacillus thermoleovorans IT-08

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.10 CA.7: 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.32

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: D.14, F.31, F.73, A.74, I.120, D.121, E.177, T.197, R.269 Ligands: GOL.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.74, A:D.121, A:E.177, A:R.269, A:R.269 Water bridges: A:D.121 GOL.3: 8 residues within 4Å: Chain A: E.177, G.196, T.197, E.198, F.480 Chain B: Y.261 Ligands: GOL.2, GOL.4 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.177, A:T.197, B:Y.261 GOL.4: 4 residues within 4Å: Chain A: R.69, F.480 Chain B: Y.261 Ligands: GOL.3 No protein-ligand interaction detected (PLIP) GOL.5: 4 residues within 4Å: Chain A: R.257, I.259, F.371, P.446 2 PLIP interactions: 2 interactions with chain A Water bridges: A:P.232, A:R.257 GOL.6: 5 residues within 4Å: Chain A: V.184, N.185, Q.243, W.249, W.278 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.185, A:Q.243 GOL.8: 10 residues within 4Å: Chain B: D.14, F.31, F.73, A.74, I.120, D.121, E.177, T.197, R.269 Ligands: GOL.9 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.74, B:D.121, B:E.177, B:R.269, B:R.269 Water bridges: B:D.121, B:T.197, B:H.238, B:H.238 GOL.9: 8 residues within 4Å: Chain A: Y.261 Chain B: E.177, G.196, T.197, E.198, F.480 Ligands: GOL.8, GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.177, B:T.197 GOL.10: 4 residues within 4Å: Chain A: Y.261 Chain B: R.69, F.480 Ligands: GOL.9 No protein-ligand interaction detected (PLIP) GOL.11: 4 residues within 4Å: Chain B: R.257, I.259, F.371, P.446 2 PLIP interactions: 2 interactions with chain B Water bridges: B:P.232, B:R.257 GOL.12: 5 residues within 4Å: Chain B: V.184, N.185, Q.243, W.249, W.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.185, B:Q.243

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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