5ei9_F : 3D-footprint complex

structure name	HUMAN PRDM9 ALLELE-A ZNF DOMAIN WITH ASSOCIATED RECOMBINATION HOTSPOT DNA SEQUENCE I (Histone-lysine N-methyltransferase PRDM9)
reference	Horton et al. 'Genes 30 257 2016
source	Homo sapiens
experiment	X-ray (resolution=1.92, R-factor=0.215)
structural superfamily	beta-beta-alpha zinc fingers;
sequence family	Zinc finger, C2H2 type;
redundant complexes	5egb_A 5eh2_E 5v3g_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5ei9_F interface=14,16,17,20,42,44,45,48,69,70,72,73,76,98,99,100,101,104, kpyvcrecgrgfsNkSHllRhqrthtgekpyvcrecgrgfrDkSHllRhqrthtgekpyvcrecgrgfRDkSNllShqrthtgekpyvcrecgrgfsNKSHllRhqrtht
interface signature	NSHRDSHRRDSNSNKSHR

Estimated binding specificities ?

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# IC=16.204 IC/col=1.157 n_of_columns=14

specificity:

A |  12   0   0   0   0   0   0   0   0  84  12   0   0  72
C |  12   0  96  96   0  96  96  96   0   0   0  96  96  12
G |  12  96   0   0   0   0   0   0   0  12  84   0   0  12
T |  60   0   0   0  96   0   0   0  96   0   0   0   0   0

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Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: PRDM9
NCCNCCNTNNCCNCN	PubMed	5ei9_F(2.26e-03), 5egb_A(1.10e-03)

Dendrogram of similar interfaces ?

matrix format

  
  ITSTSTHTRG--RG----EARA----TTTGEC--RG--RG----ET----   L   +-----------------------------5v3j_F    
                                                           !  
  --NGSGHGRG--DA--SCHGRGRGDC--SCNA------NCKTSAHG--RG   L   !                                   +5ei9_F    
                                                           !                    +--------------1 
  --DCSCQGKTTTAT--SCSC----DC--SGATRARG--RG--DCNA----   L   !                    !              +6ml4_A    
                                                           !                +---3 
  ----SA--MT--VT----NARG------ETTG------YG--ST------       !                !   !           +--6e94_A    
                                                           !             +--4   +-----------2 
  --ECSGKGRG--DG--YCKGRG--QA----TC------RA--SCDC--VT   L   !             !  !               +--5k5h_A    
                                                         -11           +-5  ! 
  NGKTWTKG--------HTHGRGTGTT--ACNA--KGRG------------   L   !           ! !  +------------------1tf3_A    
                                                           !         +-6 ! 
  ------------------------QA----TC--RG--RG--YCRT----   L   !         ! ! +---------------------7txc_E    
                                                           !       +-7 ! 
  --KGWTKA--------HCHGRG--TA--ACNA--KG--------------   L   !       ! ! +----------------------1tf6_A    
                                                           !    +--8 ! 
  ----------------------RGST--YGYC------QC--TGSTRGYT       !    !  ! +-----------------------4is1_C    
                                                           !  +-9  ! 
  ----------QT--AG--KGRG--RG--DCKG------------------   L   !  ! !  +------------------------7n5w_A    
                                                           +-10 ! 
  ----TCSGRG--LT--ETYC----NTYGQG--------------------   L      ! +---------------------------6dfb_A    
                                                              !  
  FT--KAYT----WT--WTSTET--FTVASGDC------------------   L      +---------------------------6jnm_A

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updated Fri Sep 13 19:31:11 2024