5ZQF Isomerase Dna date Apr 18, 2018
title Crystal Structure Of Human Topoisomerase II Beta In Complex Iodouridine-Containing-Dna In Space Group P3221
authors S.F.Chen, Y.R.Wang, N.L.Chan
compound source
Molecule: Dna Topoisomerase 2-Beta
Chain: A
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 Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet51b

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dnarna (5'-D(Papgpc)-R(P(Iu))-D(Pcpgpgpc R(P(Iu))-3');
Chain: C
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 32 2 1
R_factor 0.203 R_Free 0.247
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.990 94.990 231.486 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.87 Å
ligand IU, MN enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural insights into the gating of DNA passage by the topoisomerase II DNA-gate., Chen SF, Huang NL, Lin JH, Wu CC, Wang YR, Yu YJ, Gilson MK, Chan NL, Nat Commun. 2018 Aug 6;9(1):3085. doi: 10.1038/s41467-018-05406-y. PMID:30082834
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (251 Kb) [Save to disk]
  • Biological Unit Coordinates (5zqf.pdb1.gz) 481 Kb
  • LPC: Ligand-Protein Contacts for 5ZQF
  • CSU: Contacts of Structural Units for 5ZQF
  • Structure Factors (299 Kb)
  • Retrieve 5ZQF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5ZQF from S2C, [Save to disk]
  • View 5ZQF 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 5ZQF
  • 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: [5zqf_C] [5zqf_B] [5zqf_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5ZQF
  • Community annotation for 5ZQF at PDBWiki (http://pdbwiki.org)

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