5jk0_B : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF XERH SITE-SPECIFIC RECOMBINASE BOUND TO DIFH SUBSTRATE: PRE-CLEAVAGE COMPLEX (Tyrosine recombinase XerH)
reference	Barabas et al. Elife 5 ? 2016
source	Helicobacter pylori (strain ATCC 700392 / 26695) / Helicobacter pylori (strain ATCC 700392 / 26695)
experiment	X-ray (resolution=2.10, R-factor=0.193)
structural superfamily	DNA breaking-rejoining enzymes;
sequence family	Phage integrase family;
redundant complexes	5jjv_B
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5jk0_B interface=65,66,70,73,74,75,119,120,122,123,126,269,270,271,272,274,275,325, mkhpleelkdptenlllwigrflrykctslsnsqvkdqnkvfeclnelnqacsssqlekvckkaRNaglLgiNTYalpllkfheyfskarlitfnslknidevmlaeflsvytgglslATkKNyrIallglfsyidkqnqdeneksyiynitlkklpthlnneelekflesidkiemsakvrarnrllikiivftgmrsnealqlkikdftlengcytilikgkgdkyravmlkafhiesllkewlierelypvkndllfcnqkgsalTQAYlYKqveriinfaglrrekngahmlrhsfatllyqkrhdlilvqealghaslnTsriythfdkqrleeaasiwe
interface signature	RNLNTYATKNITQAYYKT

Estimated binding specificities ?

readout + contact

# IC=7.336 IC/col=0.734 n_of_columns=10

specificity:

A |   4  11  34   3   2  71  86  93  71   5
C |   5  10  19   0   3  11   3   0   9  79
G |   4   9  21   1  90   7   4   2   8   6
T |  83  66  22  92   1   7   3   1   8   6

scan!

Dendrogram of similar interfaces ?

matrix format

  
  RGNTLTNTTTYT--AATAKGNAIT------TTQAATYGYAKT--------TT   L                    +------------5jk0_B    
                                                                    +---------2 
  --------------KTTT--NARASAYT----ATVTDT--------NT--MT   L          !         +------------6en1_A    
                                                                  +-4 
  ------------TA--------------------RTLT--RT--NADAEATT   L        ! !                      +4f43_A    
                                                             +----5 +----------------------1 
  ----------------------------------RT----RT----DAEATT   L   !    !                        +4e0g_A    
                                                             !    ! 
  --------------ATST--LT------KT------TTSTRGYC--------   L --6    +-----------------------1z1b_B    
                                                             ! 
  ------------------------------RT--ET----------------       !              +-------------6gys_E    
                                                             +--------------3 
  ----------------------------------LT----------------                      +-------------3t79_A

home
updated Sat Jan 10 08:22:46 2026