› 2r2s

X-ray diffraction
2.8Å resolution

Co(III)bleomycinB2 bound to d(ATTAGTTATAACTAAT) complexed with MMLV RT catalytic fragment

Released:
DOI: 10.2210/pdb2r2s/pdb
PDB entry 2r2s coloured by chain, front view.
PDB entry 2r2s coloured by chain, side view.
PDB entry 2r2s coloured by chain, top view.
Source organism: Moloney murine leukemia virus
Primary publication:
Crystal structure of DNA-bound Co(III) bleomycin B2: Insights on intercalation and minor groove binding.
Goodwin KD, Lewis MA, Long EC, Georgiadis MM
Proc Natl Acad Sci U S A 105 5052-6 (2008)
PMID: 18362349

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115817 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Reverse transcriptase/ribonuclease H Chain: A
Molecule details ›
Chain: A
Length: 255 amino acids
Theoretical weight: 28.93 KDa
Source organism: Moloney murine leukemia virus
Expression system: Escherichia coli
UniProt:
  • Canonical: P03355 (Residues: 683-937; Coverage: 15%)
Gene name: gag-pol
Sequence domains: Reverse transcriptase (RNA-dependent DNA polymerase)
Structure domains:
DNA (5'-D(*DAP*DTP*DTP*DAP*DGP*DTP*DT)-3') Chain: B
Molecule details ›
Chain: B
Length: 7 nucleotides
Theoretical weight: 2.13 KDa
Source organism: Moloney murine leukemia virus
Expression system: Not provided
DNA (5'-D(P*DTP*DAP*DAP*DCP*DTP*DAP*DAP*DT)-3') Chain: G
Molecule details ›
Chain: G
Length: 8 nucleotides
Theoretical weight: 2.41 KDa
Source organism: Moloney murine leukemia virus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand 3CO 1 x 3CO
Ligand BLB 1 x BLB
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21212
Unit cell:
a: 52.304Å b: 144.508Å c: 50.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.228 0.228 0.308
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Revisiting bleomycin from pathophysiology to safe clinical use.
Froudarakis et al. (2013)
7 more

3 mentions without citation

Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System.
Richards et al. (2017)
2 more