› 5fbf

X-ray diffraction
1.04Å resolution

S1 nuclease from Aspergillus oryzae in complex with two molecules of 2'-deoxycytidine-5'-monophosphate

Released:
DOI: 10.2210/pdb5fbf/pdb
PDB entry 5fbf coloured by chain, front view.
PDB entry 5fbf coloured by chain, side view.
PDB entry 5fbf coloured by chain, top view.
Source organism: Aspergillus oryzae RIB40
Primary publication:
Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
Kovaľ T, Østergaard LH, Lehmbeck J, Nørgaard A, Lipovová P, Dušková J, Skálová T, Trundová M, Kolenko P, Fejfarová K, Stránský J, Švecová L, Hašek J, Dohnálek J
PLoS One 11 e0168832 (2016)
PMID: 28036383

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-150145 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nuclease S1 Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 29.08 KDa
Source organism: Aspergillus oryzae RIB40
Expression system: Aspergillus oryzae
UniProt:
  • Canonical: P24021 (Residues: 21-287; Coverage: 100%)
Gene names: AO090001000075, nucS
Sequence domains: S1/P1 Nuclease
Structure domains: P1 Nuclease

Ligands and Environments

4 bound ligands:
Ligand ZN 3 x ZN
Ligand NAG 2 x NAG
Ligand DCM 2 x DCM
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P212121
Unit cell:
a: 53.742Å b: 62.388Å c: 62.762Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.113 0.111 0.135
Expression system: Aspergillus oryzae

Quick links

Citations

2 review citations

Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned?
Erxleben A. (2019)
1 more

1 mention without citation

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
Kovaľ et al. (2016)