interface graph thumbnail
legend  pdf

structure nameSTRUCTURE OF MYCOBACTERIUM TUBERCULOSIS DNAA-DBD IN COMPLEX WITH BOX1 DNA
(Chromosomal replication initiator protein dnaA)
referenceTsodikov et al. J.Mol.Biol. 410 461 2011
sourceMycobacterium tuberculosis
experimentX-ray (resolution=2.00, R-factor=0.252)
structural superfamilyTrpR-like;
sequence familyBacterial dnaA protein helixturnhelix;
redundant complexes3pvp_B
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureKPDHTMY

Estimated binding specificities ?

readout + contactlogo
# IC=6.217 IC/col=0.777 n_of_columns=8 specificity:   
A |   0   0  16  24   0  64   0  96
C |  16   8   8  24  88  16  96   0
G |   8  88   8  24   0   8   0   0
T |  72   0  64  24   8   8   0   0
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: DNAA
TTATCCACAPubMed3pvv_B(6.57e-07), 3pvp_B(1.11e-16)
TNCACAPubMed3pvv_B(5.05e-05), 3pvp_B(4.34e-05)
TTGTCCACAPubMed3pvv_B(6.40e-12), 3pvp_B(6.96e-11)
TTTTCCACAPubMed3pvv_B(3.76e-07), 3pvp_B(1.34e-10)
TCCACAPubMed3pvv_B(5.05e-05), 3pvp_B(1.38e-08)
TTATCCAAAPubMed3pvv_B(1.53e-03), 3pvp_B(1.09e-10)
CCGTTCACAPubMed3pvv_B(3.03e-05)
TGTTATCCACAGGPubMed3pvv_B(2.26e-05), 3pvp_B(1.15e-13)
TGGATCAGPubMed3pvp_B(2.57e-05)
TCCCCAPubMed3pvp_B(3.64e-04)
TTNCACAPubMed3pvv_B(4.71e-04), 3pvp_B(4.17e-04)
TTATACACAPubMed3pvv_B(6.57e-07), 3pvp_B(1.30e-10)
CCTGTGGATAACAPubMed3pvv_B(2.26e-05), 3pvp_B(1.15e-13)
TGTGNATPubMed3pvv_B(4.71e-04), 3pvp_B(5.94e-07)
TGATCCACAPubMed3pvv_B(1.49e-03), 3pvp_B(3.53e-11)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  RALTPTDCHGTCTCLTHT------   L       +-----------------------------1j1v_A    
                                   +-1 
  ----------------NTNAIARG   L   +-2 +-----------------------------1b72_B    
                                 ! ! 
  ----------------NTNAIARG   L --3 +-----------------------------1puf_B    
                                 ! 
  ------TTLTECTASTRG------   L   +-----------------------------4i2o_B

home
updated Tue Dec 19 08:02:02 2023