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structure nameTIME-RESOLVED CRYSTAL STRUCTURE OF HINDIII WITH 230SEC SOAKING
(Type-2 restriction enzyme HindIII)
referenceKobayashi et al. 'Acta 71 256 2015
sourceHaemophilus influenzae
experimentX-ray (resolution=2.00, R-factor=0.181)
sequence familyHindIII restriction endonuclease;
multimeric complexes3a4k_AB 3a4k_CD 3wvk_AB 3wvk_CD
redundant complexes3a4k_B
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureSEKRTANKDK

Estimated binding specificities ?

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# IC=6.487 IC/col=0.927 n_of_columns=7 specificity:   
A |   9  96  96   0  22  14   0
C |  66   0   0   0  59  51   0
G |   7   0   0  96   8   0   0
T |  14   0   0   0   7  31  96
scan!

Related DNA sequences reported in the literature ?


sitesourcematches (E-value)
term: HINDIII
AAGCTTPubMed3wvk_C(1.29e-06), 2e52_AB(1.18e-08), 2e52_CD(3.65e-09), ... (total=21)
AGCTTPubMed3wvk_C(2.70e-04), 2e52_AB(3.60e-06), 2e52_CD(1.62e-06), ... (total=21)
GGCTTPubMed3wvk_C(2.70e-06), 2e52_AB(2.91e-03), 2e52_CD(1.77e-03), ... (total=21)
AGCCTPubMed3wvk_C(3.02e-06), 2e52_CD(9.72e-03), 3a4k_AB(9.72e-03), ... (total=20)
AATCTTPubMed3wvk_C(3.93e-03), 2e52_AB(3.29e-04), 2e52_CD(1.66e-04), ... (total=17)
AAGGTTPubMed3wvk_C(6.41e-03), 2e52_AB(3.29e-04), 2e52_CD(1.66e-04), ... (total=17)
AGCGTPubMed2e52_CD(9.72e-03), 3a4k_AB(9.72e-03), 3a4k_CD(9.72e-03), ... (total=18)
ATAAGPubMed2e52_AB(3.44e-03), 3wvp_C(1.07e-03), 3a4k_B(1.01e-03), ... (total=4)
TGCTTPubMed3wvk_C(1.04e-03), 2e52_AB(2.91e-03), 2e52_CD(1.77e-03), ... (total=21)
AGCTCPubMed2e52_AB(2.91e-03), 2e52_CD(1.77e-03), 3a4k_AB(1.77e-03), ... (total=16)
ATCTTPubMed2e52_CD(9.72e-03), 3a4k_AB(9.72e-03), 3a4k_CD(9.72e-03), ... (total=15)
AAGTTTPubMed3wvk_C(6.41e-03), 2e52_AB(3.29e-04), 2e52_CD(1.66e-04), ... (total=18)
TTTCAATCTTTTTATTTPubMed3wvk_C(8.50e-03), 2e52_AB(5.90e-03)
AGTAAGPubMed2e52_AB(1.17e-02), 3wvp_C(3.56e-03), 3a4k_B(3.39e-03), ... (total=4)
AGCATPubMed2e52_CD(9.72e-03), 3a4k_AB(9.72e-03), 3a4k_CD(9.72e-03), ... (total=18)
CTACTAACGCTTGGCTGGCAPubMed3wvk_C(9.53e-04), 2e52_AB(1.24e-04), 3wvg_C(5.71e-04), ... (total=4)
sitesourcematches (E-value)

Dendrogram of similar interfaces ?

matrix format
  
  ST--EAKT--------RCTTATNA--KGDCKA   L         +---------------------3wvk_C    
                                           +---2 
  --QGRCSGAAEA----------RGECRG----   L     !   +---------------------2gb7_A    
                                         +-3 
  ------------NC------------TT----   L   ! !                       +-1sx5_A    
                                       --4 +-----------------------1 
  ------------NC------------TT----   L   !                         +-2ge5_B    
                                         ! 
  ----TAKT------WC----------------   L   +---------------------------2ost_A

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updated Tue Dec 19 08:28:11 2023