SMTL ID : 2bfg.1 (1 other biounit)

crystal structure of beta-xylosidase (fam GH39) in complex with dinitrophenyl-beta-xyloside and covalently bound xyloside

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain D: G.25, R.26, L.29, W.117, E.323, E.324 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:R.26, D:R.26, D:W.117, D:E.323, D:E.324 Water bridges: D:E.324 NA.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.12: 6 residues within 4Å: Chain C: G.25, R.26, L.29, W.117, E.323, E.324 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.26, C:R.26, C:W.117, C:E.323, C:E.324

2 x ANX: 2,5-DINITROPHENOL(Non-covalent)(Covalent)

ANX.2: 6 residues within 4Å: Chain A: L.163, F.166, C.201, Y.283 Ligands: XYP.3, XYS.4 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.166, A:Y.283 ANX.13: 7 residues within 4Å: Chain D: L.163, F.166, C.201, Y.230, Y.283 Ligands: XYP.14, XYS.15 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.163, D:F.166 pi-Stacking: D:Y.283

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

XYP.3: 14 residues within 4Å: Chain A: H.54, F.115, N.159, F.166, C.201, H.228, Y.230, E.278, Y.283, W.316, E.324, F.336 Ligands: ANX.2, XYS.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.54, A:N.159, A:Y.230, A:E.324 XYP.14: 14 residues within 4Å: Chain D: H.54, F.115, N.159, F.166, H.228, Y.230, E.278, Y.283, W.316, F.322, E.324, F.336 Ligands: ANX.13, XYS.15 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.159, D:H.228, D:E.324

4 x XYS: alpha-D-xylopyranose(Post Translational Modification)

XYS.4: 13 residues within 4Å: Chain A: H.54, F.115, N.159, F.166, H.228, Y.230, E.278, Y.283, W.316, E.324, F.336 Ligands: ANX.2, XYP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.54, A:N.159, A:Y.230, A:E.324 XYS.7: 12 residues within 4Å: Chain B: H.54, F.115, N.159, F.166, H.228, Y.230, E.278, Y.283, W.316, F.322, E.324, F.336 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.54, B:N.159, B:N.159, B:Y.230, B:E.324 XYS.10: 12 residues within 4Å: Chain C: H.54, F.115, N.159, F.166, H.228, Y.230, E.278, Y.283, W.316, F.322, E.324, F.336 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:H.54, C:N.159, C:H.228, C:E.324 XYS.15: 13 residues within 4Å: Chain D: H.54, F.115, N.159, F.166, H.228, Y.230, E.278, Y.283, W.316, E.324, F.336 Ligands: ANX.13, XYP.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.159, D:H.228, D:E.324

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

SO4.5: 5 residues within 4Å: Chain A: L.358, G.359, D.360, R.374, K.375 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.358, A:D.360, A:K.375 Salt bridges: A:K.375 SO4.8: 5 residues within 4Å: Chain B: G.359, D.360, R.373, R.374, K.375 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.358, B:D.360, B:K.375 Salt bridges: B:K.375 SO4.11: 4 residues within 4Å: Chain C: G.359, D.360, R.374, K.375 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.360, C:K.375 Salt bridges: C:K.375 SO4.16: 5 residues within 4Å: Chain D: G.359, D.360, R.373, R.374, K.375 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.360, D:K.375 Salt bridges: D:K.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Czjzek, M. et al., Enzyme-Substrate Complex Structures of a Gh39 Beta-Xylosidase from Geobacillus Stearothermophilus. J.Mol.Biol. (2005)

Release Date

2005-10-12

Peptides

BETA-XYLOSIDASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BETA-XYLOSIDASE

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