1CKT Gene Regulation Dna date Apr 23, 1999
title Crystal Structure Of Hmg1 Domain A Bound To A Cisplatin-Modi Duplex
authors U.M.Ohndorf, M.A.Rould, C.O.Pabo, S.J.Lippard
compound source
Molecule: Dna (5'-D(Cpcp(5iu) Pcptpcptpgpgpapcpcptptpcpc)-3');
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Gpgpapapgpgptpcpcpapgpapgp 3');
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: High Mobility Group 1 Protein
Chain: A
Fragment: Residues 8-78, Domain A
Synonym: Hmg-1, Amphoterin, Heparin-Binding Protein P30
Engineered: Yes

Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Strain: Soragye-Dawley
Tissue: Liver
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_plasmid: Pt7-Hmg1ba
Expression_system_gene: Hmg1 Domain A (M1-F89)
symmetry Space Group: C 1 2 1
R_factor 0.238 R_Free 0.239
crystal
cell
length a length b length c angle alpha angle beta angle gamma
105.210 50.410 53.130 90.00 99.82 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand 5IU, CPT enzyme
note 1CKT is a representative structure
related structures by homologous chain: 1J3X
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceBasis for recognition of cisplatin-modified DNA by high-mobility-group proteins., Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ, Nature 1999 Jun 17;399(6737):708-12. PMID:10385126
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (31 Kb) [Save to disk]
  • Biological Unit Coordinates (1ckt.pdb1.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 1CKT
  • CSU: Contacts of Structural Units for 1CKT
  • Likely Quarternary Molecular Structure file(s) for 1CKT
  • Retrieve 1CKT in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1CKT from S2C, [Save to disk]
  • View 1CKT in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1CKT
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1CKT, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ckta_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1ckt from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ckt] [1ckt_B] [1ckt_A] [1ckt_C]
  • SWISS-PROT database: [P63159]
  • Domain organization of [HMGB1_RAT] by SWISSPFAM
  • Domain found in 1CKT: [HMG ] by SMART
  • Other resources with information on 1CKT
  • Community annotation for 1CKT at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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