› 5usa

X-ray diffraction
1.8Å resolution

5-Se-T2-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

Released:
DOI: 10.2210/pdb5usa/pdb
PDB entry 5usa coloured by chain, front view.
PDB entry 5usa coloured by chain, side view.
PDB entry 5usa coloured by chain, top view.
Source organisms:
Primary publication:
Synthesis of Pyrimidine Modified Seleno-DNA as a Novel Approach to Antisense Candidate
Fang Z, Dantsu Y, Chen C, Zhang W, Huang Z
Chemistryselect 8 (2023)

Function and Biology Details

Reaction catalysed: 
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119230 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (3 distinct):
Ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Alkalihalobacillus halodurans C-125
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: Q9KEI9 (Residues: 59-196; Coverage: 70%)
Gene names: BH0863, rnhA
Structure domains: Ribonuclease H-like superfamily/Ribonuclease H
DNA (5'-D(*AP*(T5S)P*GP*TP*CP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.9 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3') Chain: B
Molecule details ›
Chain: B
Length: 6 nucleotides
Theoretical weight: 1.88 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand T5S 1 x T5S

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: C2
Unit cell:
a: 81.201Å b: 37.731Å c: 62.238Å
α: 90° β: 96.38° γ: 90°
R-values:
R R work R free
0.191 0.19 0.216
Expression systems:
  • Escherichia coli K-12
  • Not provided

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