3L4K Isomerase Dna date Dec 20, 2009
title Topoisomerase II-Dna Cleavage Complex, Metal-Bound
authors B.H.Schmidt, A.B.Burgin, J.E.Deweese, N.Osheroff, J.M.Berger
compound source
Molecule: Dna Topoisomerase 2
Chain: A
Fragment: Residues 421-1177
Synonym: Dna Topoisomerase II
Ec: 5.99.1.3
Engineered: Yes
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast,Lager Beer Yeast,Yeast
Organism_taxid: 4932
Gene: N2244, Top2, Tor3, Ynl088w
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_strain: Bcy123
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgal

Molecule: Dna (5'-D(Pcpcptpapcptpgpcptpapc)-3')
Chain: B
Engineered: Yes
Synthetic: Yes

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

Molecule: Dna (5'-D(Pgpgpaptpgpapcpgpaptp)-3')
Chain: D
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'-D(Cpgpcpgpapaptpcpgptpcpaptp 3');
Chain: E
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 21 2 21
R_factor 0.239 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
86.064 91.851 115.939 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.98 Å
ligand PTR, TSP, ZN enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceA novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases., Schmidt BH, Burgin AB, Deweese JE, Osheroff N, Berger JM, Nature. 2010 Jun 3;465(7298):641-4. PMID:20485342
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (147 Kb) [Save to disk]
  • Biological Unit Coordinates (3l4k.pdb1.gz) 141 Kb
  • LPC: Ligand-Protein Contacts for 3L4K
  • CSU: Contacts of Structural Units for 3L4K
  • Structure Factors (371 Kb)
  • Retrieve 3L4K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3L4K from S2C, [Save to disk]
    • View 3L4K 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 3L4K
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3L4K, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3l4k_B] [3l4k_D] [3l4k] [3l4k_E] [3l4k_C] [3l4k_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3L4K: [TOP2c] [TOP4c ] by SMART
    • Other resources with information on 3L4K
  • Community annotation for 3L4K 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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