4G0U Isomerase Dna Isomerase Inhibitor date Jul 10, 2012
title Human Topoisomerase Iibeta In Complex With Dna And Amsacrine
authors C.C.Wu, T.K.Li, Y.C.Li, N.L.Chan
compound source
Molecule: Dna Topoisomerase 2-Beta
Chain: A, B
Fragment: Htop2beta Cleavage Core, Unp Residues 450-1206
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
Expression_system_strain: Bl21 Star (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet51b

Molecule: Dna (5'-D(Papgpcpcpgpapgpc)-3')
Chain: C, E
Engineered: Yes

Synthetic: Yes

Molecule: Dna (5'-D(Ptpgpcpapgpcptpcpgpgpcpt)-3
Chain: D, F
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1 21 1
R_factor 0.156 R_Free 0.213
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.923 175.800 93.130 90.00 113.61 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand ASW, MG enzyme Isomerase E.C.5.99.1.3 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceOn the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs., Wu CC, Li YC, Wang YR, Li TK, Chan NL, Nucleic Acids Res. 2013 Sep 14. PMID:24038465
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (254 Kb) [Save to disk]
  • Biological Unit Coordinates (4g0u.pdb1.gz) 245 Kb
  • LPC: Ligand-Protein Contacts for 4G0U
  • CSU: Contacts of Structural Units for 4G0U
  • Structure Factors (492 Kb)
  • Retrieve 4G0U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4G0U from S2C, [Save to disk]
  • Re-refined 4g0u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4G0U 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 4G0U
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4G0U, from MSDmotif at EBI
  • Fold representative 4g0u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4g0u_B] [4g0u_F] [4g0u_A] [4g0u_C] [4g0u_D] [4g0u] [4g0u_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4G0U: [TOP2c] [TOP4c ] by SMART
  • Other resources with information on 4G0U
  • Community annotation for 4G0U at PDBWiki (http://pdbwiki.org)

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