5ipl_F : 3D-footprint complex

structure name	SIGMAS-TRANSCRIPTION INITIATION COMPLEX WITH 4-NT NASCENT RNA (RNA POLYMERASE SIGMA FACTOR RPOS)
reference	Steitz et al. Proc.Natl.Acad.Sci.USA 113 4051 2016
source	ESCHERICHIA COLI
experiment	X-ray (resolution=3.60, R-factor=0.249)
structural superfamily	Sigma2 domain of RNA polymerase sigma factors;Sigma3 and sigma4 domains of RNA polymerase sigma factors;
sequence family	Sigma70 region 3; Sigma70 region 2; Sigma70, region 4; Sigma70 factor, region 12;
redundant complexes	5ipn 5ipm
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 5ipl_F interface=6,7,10,15,18,24,46,48,49,60,82,83,86,88,89,91,92,93,95,96,97,99,100,103,104,106,107,110,111,117,118,120,121,124,127,166,172,174,177,179,180, rvldaTQlyLgeigYspLltaeeEvyfarralrgdvasrrrmiesNlRLvvkiarrygnRglalldlieegnlgliravekFDpeRgFRfSTYaTWWiRQtiERaIMnqTRtirlpIHiVKelNvyLrtarelshkldhepsaeeiaeqldkpvddvsrmlrlneRitsvdTpLggDsEKalldiladekengpedttqdddmkqsivkwlfelnakqrevlarrfgllgyeaatledvgreigltrervrqiqveglrrlreilqtqglniealfl
interface signature	TQLYLENRLRFDRFRSTYTWWRQERIMTRIHVKNLRTLDEK

Estimated binding specificities ?

contact

# IC=18.665 IC/col=1.167 n_of_columns=16

specificity:

A |   0   9  69   0   0  96   0   0  96   0  96   0   9  96   0  96
C |   0   9   9   0   0   0   0   0   0   0   0   0  67   0   0   0
G |  96  11   9  96  96   0   0   0   0   0   0  96  11   0   0   0
T |   0  67   9   0   0   0  96  96   0  96   0   0   9   0  96   0

scan!

Dendrogram of similar interfaces ?

matrix format

  
  DGVGRGLGLTNTRGLT------RC------FADA--KAYA--SCTAYATCWTWT--QT----VTHTEARCRCECEGIASAQAICEGDGSG--FG--------TTRGECRTRCQT------   L                           +-----6edt_F    
                                                                                                                                                 +-------2 
  --------LTNTRTLT--------------FADA--KAYAKTSTTAYATCWTWC--QCTARGVTHTEC------------------------------LG--TTRGECRCRTQT------   L                   !       !     +5tw1_F    
                                                                                                                                   +-------------3       +-----1 
  ----------NTRGLT------------KTFAEA--RAFAKTSATAYTTA--WTRA--------------------------IGEGDGSG--FG--------------------------         !             !             +4oin_F    
                                                                                                                                   !             ! 
  ----------NTRTLT--------------FAEA--RAFAKTSTTAYATCWTWCRAQTNARGVTHTEG------------------------------LG--TTRTECRCRTQT------   L     !             +-------------4xlp_F    
                                                                                                                                 +-7 
  ----------NTRTLT--------------FAEA--RAYA--STTAYATAWTWTRAQT--RT--HGEA----------------------------------------------------   L   ! !     +----------------------6n61_F    
                                                                                                                                 ! !   +-5 
  ------------------------------------------------------------------------------------------SG----------------------------       ! !   ! +----------------------6dvc_F    
                                                                                                                               --8 +---6 
  ----------------DGQGLGMARTPG--FT--RT--TTNT----------------------------------------------------PCFCYG--------TGMGSG--RGQC   L   !     !        +--------------5zx2_F    
                                                                                                                                 !     +--------4 
  --------------------------------------------------------------------------------------------------YG--------TGRGSGFTRG--   L   !              +--------------2h27_A    
                                                                                                                                 ! 
  --------------------------------------------------------------------------------------------------LTETTTRAECRCRCQC------   L   +----------------------------3n97_A

home
updated Mon Dec 18 12:56:08 2023