› 6sxr

X-ray diffraction
1.64Å resolution

E221Q mutant of GH54 a-l-arabinofuranosidase soaked with 4-nitrophenyl a-l-arabinofuranoside

Released:
DOI: 10.2210/pdb6sxr/pdb
PDB entry 6sxr coloured by chain, front view.
PDB entry 6sxr coloured by chain, side view.
PDB entry 6sxr coloured by chain, top view.
Source organism: Aspergillus luchuensis IFO 4308
Primary publication:
Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining α-l-Arabinofuranosidases.
McGregor NGS, Artola M, Nin-Hill A, Linzel D, Haon M, Reijngoud J, Ram A, Rosso MN, van der Marel GA, Codée JDC, van Wezel GP, Berrin JG, Rovira C, Overkleeft HS, Davies GJ
OpenAccess logo J Am Chem Soc 142 4648-4662 (2020)
PMID: 32053363

Function and Biology Details

Reaction catalysed: 
Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185582 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Alpha-L-arabinofuranosidase B Chain: A
Molecule details ›
Chain: A
Length: 482 amino acids
Theoretical weight: 50.88 KDa
Source organism: Aspergillus luchuensis IFO 4308
Expression system: Komagataella pastoris
UniProt:
  • Canonical: Q8NK89 (Residues: 19-499; Coverage: 100%)
Gene names: AKAW_08685, abfB
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
8 bound ligands:
Ligand NAG 1 x NAG
Ligand SO4 3 x SO4
Ligand ACT 2 x ACT
Ligand KHP 3 x KHP
Ligand EDO 13 x EDO
Ligand PEG 8 x PEG
Ligand PGE 1 x PGE
Ligand 1PE 2 x 1PE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: R32
Unit cell:
a: 111.97Å b: 111.97Å c: 341.39Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.161 0.16 0.181
Expression system: Komagataella pastoris

Quick links

Citations

4 review citations

Plant Glycosides and Glycosidases: A Treasure-Trove for Therapeutics.
Kytidou et al. (2020)
3 more

1 mention without citation

Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining α-l-Arabinofuranosidases.
McGregor et al. (2020)