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structure nameARCHAEAL INTRON-ENCODED HOMING ENDONUCLEASE I-VDI141I COMPLEXED WITH DNA
(RRNA intron-encoded endonuclease)
referenceStoddard et al. 'Nucleic 36 6988 2008
sourceVulcanisaeta distributa
experimentX-ray (resolution=2.50, R-factor=0.231)
structural superfamilyHoming endonucleases;
sequence familyLAGLIDADG endonuclease;
multimeric complexes3e54_AB
links to other resourcesNAKB PDBSum PDIdb DNAproDB
protein sequence
interface signatureSSSKQDVRDTRMKAQDKY

Estimated binding specificities ?

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# IC=13.150 IC/col=1.096 n_of_columns=12 specificity:   
A |   0  96  96   0  69   8  88   0   8   0  96   0
C |   0   0   0   0   8  11   0   0   8  96   0   0
G |   0   0   0  96   8  69   8  96  11   0   0  96
T |  96   0   0   0  11   8   0   0  69   0   0   0
scan!

Dendrogram of similar interfaces ?

matrix format
  
  SANCSCKG--LT--------------DAECTG------RC--KGST------------DAQA----QCNT   L                      +-------2ex5_A    
                                                                                    +------------14  
  CA--QGVT--RG--DCYA--------RT--FA------RG------RGNTDTMCEA--------KT----   L        !             !     +-5a74_B    
                                                                                    !             +----11  
  SAIAQA--------SC------RG--KG--TA----YC----------ST--VA--------KTTT----   L        !                   +-2vbl_B    
                                                                                    !  
  SGIGQAKG--NC--SC------RG--QG--TA----YCAT--------SC--VCKGRG------TT----   L        !                         +6fb0_A    
                                                                                    !                       +-1 
  STITQAKG--RG--STNT----QT--ST--TC------YT--------SC--VCDTRGST--KGTG----   L        !                     +-2 +3mxb_B    
                                                                                    !                     ! ! 
  STITQANG--NT--SC------RG--RG--TC------RG------------VCQT--------TT----   L   +---16                  +-10 +2xe0_A    
                                                                               !    !                  !  !  
  SAYCLCIT--RGDCYA------QG------IG----NARG----RG----DTIC--RG------------   L   !    !                  !  ! +2fld_B    
                                                                               !    !      +----------12  +-3 
  SAYCKTITPTRGDCYA--------------IG----NARG----RT----DTICDG--IA----------   L   !    !      !           !    +3fd2_A    
                                                                               !    !      !           !  
  STITQA--------ST------RG--RG--TC----YCRG--------SG--VAQT--------TC----   L   !    !      !           +--3mxa_A    
                                                                               !    !      !  
  ST--NAVT--HG--TCNA----AT--LCYCAT------YG--NA----SADCTCKTKGSA----------   L   !    !      !             +4lq0_A    
                                                                               !    +-----15             ! 
  SA--RGRG--NT--KTST----ST--EC--TA--------------ST----AT--KG------------   L   !           !             !     +6bd0_A    
                                                                               !           !          +--9   +-4 
  SA--RARG--RG--KT----------EC--KG--------------ST----ATRGRG------------   L -17           !          !  ! +-6 +6uw0_B    
                                                                               !           !          !  ! ! ! 
  STIGRGRG--------MC----LT--EC--KG------TT------NA------MGRTSC----------   L   !           !          !  +-7 +5t2n_A    
                                                                               !           !          !    ! 
  STMG----------KGYC----RT----RGSA------FC------------STQTRGEC----------   L   !           +---------13    ! +5esp_A    
                                                                               !                      !    +-5 
  SALTRGRG--NT--KT------ST--EC--TAHAKA----------ST--------KGTC----------   L   !                      !      +6uwj_A    
                                                                               !                      !  
  CGRGSTTT----------KARGQT--FAQGNG----------HC--SC----LAQGRGQA----------   L   !                      !   +4yit_A    
                                                                               !                      +---8 
  --MGTASG--------RA----ST--RGRG----------------------DTRGRCEC----------   L   !                          +6bce_A    
                                                                               !  
  --YT------------------RGSGECRGVTTG------QG--VG--------EARGSC----------   L   +--------------------------2vs7_A    
                                                                             

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updated Tue Dec 19 07:16:05 2023