5ZAD Dna Binding Protein Dna date Feb 07, 2018
title Human Topoisomerase II Beta In Complex With Dna
authors L.Y.Sun, L.W.Zhu, Y.J.Tang
compound source
Molecule: Dna Topoisomerase 2-Beta
Chain: A, B
Synonym: Dna Topoisomerase II,Beta Isozyme
Ec: 5.99.1.3
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Top2b
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (5'-D(Papgpcpcpgpapgpc)-3')
Chain: C, D
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Ptpgpcpapgpcptpcpgpgpcpt)-3
Chain: F, E
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 32
R_factor 0.180 R_Free 0.227
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.006 95.006 230.289 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.54 Å
ligand
enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceIncreasing the distance between two monomers of topoisomerase IIbeta under the action of antitumor agent 4beta-sulfur-(benzimidazole) 4'-demethylepipodophyllotoxin., Sun LY, Zhu LW, Tang YJ, Sci Rep. 2018 Oct 8;8(1):14949. doi: 10.1038/s41598-018-33366-2. PMID:30297860
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (543 Kb) [Save to disk]
  • Biological Unit Coordinates (5zad.pdb1.gz) 536 Kb
  • CSU: Contacts of Structural Units for 5ZAD
  • Structure Factors (1685 Kb)
  • Retrieve 5ZAD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZAD from S2C, [Save to disk]
    • View 5ZAD 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 5ZAD
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5zad_B] [5zad_A] [5zad_E] [5zad_F] [5zad_C] [5zad_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5ZAD
  • Community annotation for 5ZAD at PDBWiki (http://pdbwiki.org)

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