4R1F Re-refined Human DNA topoisomerase IIa (ATPase and transducer domains) in complex with ADP and SO4 date
authors Stanger, F.V., Schirmer, T.
compound source
symmetry
R_factor
R_Free 0.2434
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.51
ligand ADP, GOL, MG, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceStructure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis., Stanger FV, Dehio C, Schirmer T, PLoS One. 2014 Sep 9;9(9):e107289. doi: 10.1371/journal.pone.0107289. eCollection, 2014. PMID:25202966
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (255 Kb) [Save to disk]
  • Biological Unit Coordinates (4r1f.pdb1.gz) 127 Kb
  • Biological Unit Coordinates (4r1f.pdb2.gz) 127 Kb
  • LPC: Ligand-Protein Contacts for 4R1F
  • CSU: Contacts of Structural Units for 4R1F
  • Structure Factors (511 Kb)
  • Retrieve 4R1F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R1F from S2C, [Save to disk]
  • Re-refined 4r1f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R1F 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 4R1F
  • 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 4R1F, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r1f_B] [4r1f_A] [4r1f_C] [4r1f_D] [4r1f]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4R1F: [HATPase_c] [TOP2c ] by SMART
  • Other resources with information on 4R1F
  • Community annotation for 4R1F at PDBWiki (http://pdbwiki.org)

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