4FM9 Isomerase Dna date Jun 15, 2012
title Human Topoisomerase II Alpha Bound To Dna
authors T.J.Wendorff, B.H.Schmidt, P.Heslop, C.A.Austin, J.M.Berger
compound source
Molecule: Dna Topoisomerase 2-Alpha
Chain: A
Fragment: Residues 431-1193
Synonym: Dna Topoisomerase II, Alpha Isozyme
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Top2, Top2a
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(Pgpapgpgpaptpgpapcpgpaptpg
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 2 2 21
R_factor 0.227 R_Free 0.270
length a length b length c angle alpha angle beta angle gamma
85.918 215.081 128.650 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand GOL, MG enzyme Isomerase E.C. BRENDA

Primary referenceThe Structure of DNA-Bound Human Topoisomerase II Alpha: Conformational Mechanisms for Coordinating Inter-Subunit Interactions with DNA Cleavage., Wendorff TJ, Schmidt BH, Heslop P, Austin CA, Berger JM, J Mol Biol. 2012 Dec 7;424(3-4):109-24. doi: 10.1016/j.jmb.2012.07.014. Epub 2012, Jul 25. PMID:22841979
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (283 Kb) [Save to disk]
  • Biological Unit Coordinates (4fm9.pdb1.gz) 550 Kb
  • LPC: Ligand-Protein Contacts for 4FM9
  • CSU: Contacts of Structural Units for 4FM9
  • Structure Factors (304 Kb)
  • Retrieve 4FM9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4FM9 from S2C, [Save to disk]
  • Re-refined 4fm9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4FM9 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 4FM9
  • 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 4FM9, from MSDmotif at EBI
  • Fold representative 4fm9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4fm9_C] [4fm9_A] [4fm9] [4fm9_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4FM9: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 4FM9
  • Community annotation for 4FM9 at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science