interface graph thumbnail
legend  pdf

structure nameSTRUCTURE OF VARIOLA TOPOISOMERASE NON-COVALENTLY BOUND TO DNA
(DNA topoisomerase 1)
referenceVan Duyne et al. Mol.Cell 23 343 2006
sourceVariola virus
experimentX-ray (resolution=1.90, R-factor=0.199)
structural superfamilyDNA breaking-rejoining enzymes;DNA topoisomerase I domain;
sequence familyEukaryotic DNA topoisomerase I, catal; Viral DNA topoisomerase I, Nterminal;
redundant complexes2h7f_X
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureRQYYRKKYKDERY

Estimated binding specificities ?

readout + contactlogo
# IC=6.308 IC/col=0.631 n_of_columns=10 specificity:   
A |  67  96   0   0  13   7  21  34  12  74
C |   9   0   0   0  10  74  23  20  60   7
G |   9   0  96  96  63   7  31  22  12   8
T |  11   0   0   0  10   8  21  20  12   7
scan!

Dendrogram of similar interfaces ?

matrix format
  
  HTRA--QAYCYT--RT------KGKGYGKT----ETRGYG   L                   +-----------2h7g_X    
                                                       +---------1 
  ----MG--YA--KT--------NC----KTDA----TT--   L   +-----2         +-----------2b9s_A    
                                                 !     ! 
  ----------------RG--------------RG------   L --3     +---------------------3m4a_A    
                                                 ! 
  ------------------FCKC------KC------NTRG   L   +---------------------------1flo_A

home
updated Sun Aug 3 06:14:36 2025