› 1ckt

X-ray diffraction
2.5Å resolution

CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX

Released:
DOI: 10.2210/pdb1ckt/pdb
PDB entry 1ckt coloured by chain, front view.
PDB entry 1ckt coloured by chain, side view.
PDB entry 1ckt coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.
Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ
Nature 399 708-12 (1999)
PMID: 10385126

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113545 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
High mobility group protein B1 Chain: A
Molecule details ›
Chain: A
Length: 71 amino acids
Theoretical weight: 8.5 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63159 (Residues: 8-78; Coverage: 33%)
Gene names: Hmg-1, Hmg1, Hmgb1
Sequence domains: HMG-box domain
Structure domains: High mobility group box domain
DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 16 nucleotides
Theoretical weight: 4.87 KDa
Source organism: Rattus norvegicus
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 5.04 KDa
Source organism: Rattus norvegicus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CPT 1 x CPT
1 modified residue:
Ligand 5IU 1 x 5IU

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: C2
Unit cell:
a: 105.21Å b: 50.41Å c: 53.13Å
α: 90° β: 99.82° γ: 90°
R-values:
R R work R free
0.238 0.238 0.239
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

56 review citations

HMGB1 in health and disease.
Kang et al. (2014)
55 more

26 mentions without citation

Inhibition of transcription by platinum antitumor compounds.
Todd et al. (2009)
25 more