1CKT

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

Structural Biology Knowledgebase: 1CKT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.238

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1CKT

Classification: GENE REGULATION / DNA

Total Structure Weight: 18708.22


Macromolecule Entities
Molecule Chains Length Organism Details
HIGH MOBILITY GROUP 1 PROTEIN A 71 Rattus norvegicus Fragment: RESIDUES 8-78, DOMAIN A
Gene Name(s): Hmgb1 Hmg-1 Hmg1
Macromolecule Entities
Molecule Chains Length Organism Details
DNA (5'-D(*CP*CP*(5IU)P*CP*TP*CP*TP*GP*GP*AP*CP*CP*TP*TP*CP*C)-3') B 16 synthetic
DNA (5'-D(*GP*GP*AP*AP*GP*GP*TP*CP*CP*AP*GP*AP*GP*AP*GP*G)-3') C 16 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CPT
Query on CPT

B Cisplatin
diammine(dichloro)platinum (Synonym)
Cl2 H6 N2 Pt
LXZZYRPGZAFOLE-UHFFFAOYSA-L
Ligand Explorer
 
JSmol
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
5IU
Query on 5IU
B DNA LINKING C9 H12 I N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.238
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 105.21 α = 90.00
b = 50.41 β = 99.82
c = 53.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-04-23
  • Released Date: 1999-06-30
  • Deposition author(s): Ohndorf, U.-M., Rould, M.A., Pabo, C.O., Lippard, S.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update