SMTL ID : 5glp.1 (1 other biounit)

Crystal structure of CoXyl43, GH43 beta-xylosidase/alpha-arabinofuranosidase from a compostmicrobial metagenome in complex with l-arabinose, calcium-bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x CA: CALCIUM ION(Non-covalent)

CA.1: 2 residues within 4Å: Chain A: S.34, H.294 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.294, H2O.3, H2O.5, H2O.6, H2O.8

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

NA.2: 1 residues within 4Å: Chain A: T.338 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.338 Water bridges: A:I.336, A:T.338

2 x ARA: alpha-L-arabinopyranose(Non-covalent)

ARA.3: 13 residues within 4Å: Chain A: D.32, S.47, F.63, M.65, W.100, A.101, I.151, D.152, E.243, T.292, H.294, R.321 Ligands: ARA.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.47, A:A.101, A:D.152, A:H.294, A:R.321 Water bridges: A:N.293 Salt bridges: A:R.321 ARA.4: 12 residues within 4Å: Chain A: N.57, D.58, G.60, F.63, W.100, I.170, W.171, G.172, G.173, E.243, T.292 Ligands: ARA.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.58, A:D.58, A:G.60, A:I.170, A:G.172, A:G.173 Water bridges: A:D.58, A:E.243 Salt bridges: A:H.62

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: F.38, D.39, S.106, Y.111 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.38 Hydrogen bonds: A:D.39, A:S.106, A:S.106, A:Y.111 Water bridges: A:G.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matsuzawa, T. et al., Crystal structure of metagenomic beta-xylosidase/ alpha-l-arabinofuranosidase activated by calcium. J. Biochem. (2017)

Release Date

2017-03-15

Peptides

Glycoside hydrolase family 43: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glycoside hydrolase family 43

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