› 4kgc

X-ray diffraction
2.69Å resolution

Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM

Released:
DOI: 10.2210/pdb4kgc/pdb
PDB 4kgc coloured by chain and viewed from the front.
PDB 4kgc coloured by chain and viewed from the side.
PDB 4kgc coloured by chain and viewed from the top.
Source organism: Xenopus laevis
Primary publication:
Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity.
Adhireksan Z, Davey GE, Campomanes P, Groessl M, Clavel CM, Yu H, Nazarov AA, Yeo CH, Ang WH, Dr��ge P, Rothlisberger U, Dyson PJ, Davey CA
Nat Commun 5 3462 (2014)
PMID: 24637564

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
Entry contents:
4 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (6 distinct):
Histone H3.2 Chains: A, E
Molecule details ›
Chains: A, E
Length: 136 amino acids
Theoretical weight: 15.42 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P84233 (Residues: 1-136; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
Histone H4 Chains: B, F
Molecule details ›
Chains: B, F
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P62799 (Residues: 1-103; Coverage: 100%)
Sequence domains: Centromere kinetochore component CENP-T histone fold
Structure domains: Histone, subunit A
Histone H2A Chains: C, G
Molecule details ›
Chains: C, G
Length: 130 amino acids
Theoretical weight: 14.11 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6AZJ8 (Residues: 1-130; Coverage: 100%)
Gene names: LOC494591, h2ac14, h2ac14.L, hist1h2aj, hist1h2aj.L
Sequence domains:
Structure domains: Histone, subunit A
Histone H2B 1.1 Chains: D, H
Molecule details ›
Chains: D, H
Length: 126 amino acids
Theoretical weight: 13.98 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: P02281 (Residues: 1-126; Coverage: 100%)
Sequence domains: Core histone H2A/H2B/H3/H4
Structure domains: Histone, subunit A
DNA (145-mer) Chain: I
Molecule details ›
Chain: I
Length: 145 nucleotides
Theoretical weight: 44.75 KDa
DNA (145-mer) Chain: J
Molecule details ›
Chain: J
Length: 145 nucleotides
Theoretical weight: 44.74 KDa

Ligands and Environments

3 bound ligands:
Ligand HRU 4 x HRU
Ligand SO4 3 x SO4
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 106.62Å b: 109.71Å c: 181.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.248 0.248 0.282
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Frontiers of metal-coordinating drug design.
Palermo et al. (2021)
13 more

2 mentions without citation

Ligand substitutions between ruthenium-cymene compounds can control protein versus DNA targeting and anticancer activity.
Adhireksan et al. (2014)
1 more