5ffj_B : 3D-footprint complex

structure name	STRUCTURE OF A NUCLEASE-DELETION MUTANT OF THE TYPE ISP RESTRICTION- MODIFICATION ENZYME LLAGI IN COMPLEX WITH A DNA SUBSTRATE MIMIC (Endonuclease and methylase LlaGI)
reference	Saikrishnan et al. 'Nucleic 44 4396 2016
source	Lactococcus lactis
experiment	X-ray (resolution=2.84, R-factor=0.231)
structural superfamily	S-adenosyl-L-methionine-dependent methyltransferases;P-loop containing nucleoside triphosphate hydrolases;
sequence family	Type III restriction enzyme, res subunit;
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5ffj_B interface=536,687,690,692,725,727,787,788,794,800,802,804,806,807,892,895,897,955,995,996,998,1036,1037,1042,1044, lrdyqqtakenalahfkendrgqlimapgtgktftslkisealskdkngpfkvlylvpsiqlltqtlrgwnndteltitsmavtsdrdasasdigypattsskkilqnwhdfeslpkqtdmlvvfstyqsievigeaqkegfpefdfiisdeahrttgahasafskvhsnnnvkglkrmyqtatpkiygsillssmddeskygevffrmgfgqavsrdiltdykvmvrivgiwngmmrrraiaftrtieeskkvssqfeevvneylsmrhnalqkgeildwladpnkpadivsdiptldaviflspkksqvdivqavgrimrkdygyiilpivinnknyetvwqvinalrsvderfeamidklnmakqlkvwnkfegaifgkivqkvgdrkylenwskdvakiaerqinwiknklsdkkdpislefkkfvsslqhnindsidekqaaemlsqhlitkpifealfseysfvnqnpvsqamesivselekagfakeqenleplyesvrmraegiekaedkqkiivtlydkffktafiVftpievvdfivhsvddvlkkhfgkslaskdvhildpftgtgtfivrtltylkeqmdageislsditrkfmkelhaneivllsyyiaainieatfdeingeeegyvpfegivltdtfesteteetldddyfgtnderlkrqqevpitaiigNppYsKgqsnendnnknieyprlfksiadsyvknskttSvLgmydsyvlsirwasnrlndkgvigfvsngsyidsqsadglrkslfkefnhlyifnlrgdQRtqgetSrkeggKiFgSgSRtsiaisilvkddsdnhevhyhdigdyltrddkldilrdkesilnidwenispdenndwinqrdqnylnyrpladengsifsvkdIgiVtNrdawvsnfskinvsdnvqimiknynlevdrlenidvklndktvvdyvtnderkiswsRslkqraarrektqfshsdimlamyrpftkkylyrnrflnENvRktyqtfpdknsknllinisgqgdkadfatliseylsdMHviggQaRnlprftyegrtdnivsddefyyvygvlhssayrkryandlkkdlpripllknkdkyveigrklsdlhlnyenqpiwdgieveisqpdyrvkkmkhpkkgvldtiiynesitikniperayeyvvngrpaiewiidqyqvktdkksgitddpnefsdnpkyilnlllsvitvsmrtlelieelpefeiq
interface signature	VNYKSLQRSKFSSRIVNRENRMHQR

Estimated binding specificities ?

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# IC=9.518 IC/col=1.190 n_of_columns=8

specificity:

A |  14   0  96   0   0   0  96   0
C |  52  96   0   0  96  96   0   0
G |  14   0   0   0   0   0   0  96
T |  16   0   0  96   0   0   0   0

scan!

Dendrogram of similar interfaces ?

matrix format

  
  ------------------VANA--YGKT--------KAKGVA----   L                                +--------------2ih2_D    
                                                                          +---------1 
  --------------------NA--------------AAACVAYCKG   L                 +----2         +--------------5hr4_C    
                                                                     !    ! 
  ----------------------NA----------FA----VA----                   +-3    +------------------------2y7h_B    
                                                                   ! ! 
  ------------------FA----------------TATTIT----                 +-4 +-----------------------------7btq_A    
                                                                 ! ! 
  ----EG----------------------------------------               +-5 +-----------------------------6iy2_O    
                                                               ! ! 
  ------RC--------------------------------------             +-6 +-----------------------------1z63_A    
                                                             ! ! 
  ----QG--HCRT----------------------------------           +-7 +-----------------------------6gej_M    
                                                           ! ! 
  ----EG----------------------------------------         +-8 +-----------------------------6kw3_Y    
                                                         ! ! 
  --------------PGHC----------------------------   L   +-9 +-----------------------------5v9x_A    
                                                       ! ! 
  ----------------------------ECNCVC------------     -10 +-----------------------------6kdb_D    
                                                       !  
  RAYTKG------RA--------------------------------       +-----------------------------2p6r_A

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updated Tue Dec 19 10:22:31 2023