2vla_A : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE BPUJI RECOGNITION DOMAIN IN COMPLEX WITH COGNATE DNA (RESTRICTION ENDONUCLEASE R.BPUJI)
reference	Sukackaite et al. J.Mol.Biol. 378 1084 2008
source	BACILLUS PUMILUS
experiment	X-ray (resolution=1.30, R-factor=0.140)
redundant complexes	5hlt_A 5hnf_A 5hnh_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 2vla_A interface=15,17,20,63,64,67,70,71,121,202,204,208, mnynpeeqfrctiiRgKakNmldnllpayaniiddicpcdkasfvkdfnnrlieilgeettkKTldNhrTEiagklfgmfyeddevifpsgrtnkyiedsdqpaffkdicfkfqfpngmdKldkviekvgakiqirqfpyilqvlltadnnniqlskddiayyvlnslqvlqgkikpieviekiiedrsnditkkvrhpgkEtSysmQhireqlnylelanliridgnlvklnyreaeninyiaqfwgnkpefnaykydftseddkksffkdwqqyysnv
interface signature	RKNKTNTEKESQ

Estimated binding specificities ?

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# IC=7.099 IC/col=1.014 n_of_columns=7

specificity:

A |  13  96   0   0   0   0  16
C |  54   0  96   0   0   0  13
G |  16   0   0  96  96  96  13
T |  13   0   0   0   0   0  54

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: BPUJI
CCCGT	PubMed	2vla_A(7.02e-07), 5hnf_A(7.02e-07), 5hnh_A(7.02e-07), ... (total=4)

Dendrogram of similar interfaces ?

matrix format

  
  RGKG------KGTG--NCTCECKA------ETST----QA----   L        +----------------------2vla_A    
                                                     +----2 
  ----LTNTHG--RTYTPT--------------------------   L   !    !          +-----------6qil_A    
                                                   --3    +----------1 
  ------------------------RT--------NTHGTAYTRG       !               +-----------2efw_A    
                                                     ! 
  --------------------------KAFA--------------       +---------------------------3aaf_B

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updated Fri Sep 13 16:43:11 2024