1tf6_D : 3D-footprint complex

structure name	CO-CRYSTAL STRUCTURE OF XENOPUS TFIIIA ZINC FINGER DOMAIN BOUND TO THE 5S RIBOSOMAL RNA GENE INTERNAL CONTROL REGION (PROTEIN TRANSCRIPTION FACTOR IIIA)
reference	Harrison et al. Proc.Natl.Acad.Sci.USA 95 2938 1998
source	Xenopus laevis
experiment	X-ray (resolution=3.10, R-factor=0.308)
structural superfamily	beta-beta-alpha zinc fingers;
sequence family	Zinc finger, C2H2 type;
redundant complexes	1tf3
reference complex	1tf3_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 1tf6_D interface=20,22,23,52,53,56,80,82,83,86,90,142,144,145,148, pvvykryicsfadcgaaynKnWKlqahlckhtgekpfpckeegcekgftslHHltRhslthtgeknftcdsdgcdlrftTkANmkKhfnRfhnikicvyvchfencgkafkkhnqlkvhqfshtqqlpyecphegcdkrfsLpSRlkRhekvhagypckkddscsfvgktwtlylkhvaech
interface signature	KWKHHRTANKRLSRR

Estimated binding specificities ?

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# IC=12.231 IC/col=0.556 n_of_columns=22

specificity:

A |   0   7  24  24  24  24  24  24  24  24   4   0  96   0   0   0   4  64  24  71   0   0
C |   3   4  24  24  24  24  24  24  24  24   7   0   0   0   0   0   2   9  24   9  96  91
G |  66  27  24  24  24  24  24  24  24  24  34  96   0   0  96  96  83  12  24   9   0   4
T |  27  58  24  24  24  24  24  24  24  24  51   0   0  96   0   0   7  11  24   7   0   1

scan!

Related DNA sequences reported in the literature ?

site	source	matches (E-value)
term: TFIIIA
GGATGGGAG	PubMed	1tf6_D(3.73e-12), 1tf3_A(1.20e-14)
TGGGA	PubMed	1tf6_D(8.28e-05), 1tf3_A(9.73e-06)
CTCCCATCC	PubMed	1tf6_D(3.73e-12), 1tf3_A(1.20e-14)
GGATGGGAGC	PubMed	1tf6_D(2.75e-10), 1tf3_A(3.58e-13)
GCCAATCC	PubMed	1tf6_D(2.61e-03), 1tf3_A(1.79e-04)

Dendrogram of similar interfaces ?

matrix format

  
  KG--WTKA------------HCHG--RGTA--ACNAKGRGLTSTRGRG   L   +----------------1tf6_D    
                                                         ! 
  QA--TTNA------STQAQTATSTNTATTTLAHGTCRG----------   L   !                  +1g2f_F    
                                                         !                +-2 
  RG--DCHG------------KGDC--RGQARGATNA------------   L   !              +-3 +2i13_A    
                                                         !              ! ! 
  QAST--SCRG------RGSGDCHG--TTRG--DAECRG----------   L --8         +----5 +1a1h_A    
                                                         !         !    ! 
  QA--SGNAKG------QASTSCDC--KGRG--DCHARG----------   L   !         !    ! +1mey_C    
                                                         ! +-------6    +-1 
  --------KT------EC--SCKG--RGLT--FCNA------------   L   ! !       !      +1ubd_C    
                                                         ! !       ! 
  ----------------RG--DCEC--RGRG--DCHG------------   L   +-7       !    +-1f2i_J    
                                                           !       +----4 
  ----------PCYC--RG--DA----RGRG--DCHG------------   L     !            +-2prt_A    
                                                           ! 
  ----------------RGSTDCHGTTTTRG--DAECRG----------   L     +--------------1llm_D

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updated Thu Jan 8 19:15:43 2026