4yfu_D : 3D-footprint complex

structure name	CRYSTAL STRUCTURE OF OPEN BACILLUS FRAGMENT DNA POLYMERASE BOUND TO DNA AND DTTP (DNA polymerase)
reference	Structure 23 1609 2015 C10 H17 N2 O14 P3
source	Geobacillus stearothermophilus
experiment	X-ray (resolution=1.50, R-factor=0.197)
structural superfamily	DNA/RNA polymerases;Ribonuclease H-like;
sequence family	DNA polymerase family A;
multimeric complexes	6ur9_AD 6us5_AD
redundant complexes	1l3s_A 1l3t_A 1l3u_A 1l3v_A 1l5u_A 1lv5_B 1njw_A 1njx_A 1njy_A 1njz_A 1nk0_A 1nk4_A 1nk5_A 1nk6_A 1nk7_A 1nk8_A 1nk9_A 1nkb_A 1nkc_A 1nke_A 1u45_A 1u47_A 1u48_A 1u49_A 1u4b_A 1ua0_A 1ua1_A 1xc9_A 2bdp_A 2hhq_A 2hhs_A 2hht_A 2hhu_A 2hhv_A 2hhw_D 2hhx_A 2hvh_D 2hvi_A 2hw3_A 2xo7_A 2xy5_A 2xy6_A 2xy7_A 2y1i_A 2y1j_A 3bdp_A 3eyz_A 3ez5_A 3hp6_A 3hpo_A 3ht3_A 3pv8_A 3px0_D 3px4_D 3px6_D 3tan_A 3tap_A 3taq_A 3tar_A 3thv_D 3ti0_A 4b9l_A 4b9m_A 4b9n_A 4b9s_A 4b9t_A 4b9u_A 4b9v_A 4bdp_A 4dqi_A 4dqp_D 4dqq_D 4dqr_A 4dqs_A 4ds4_A 4ds5_D 4dse_D 4dsf_D 4dsi_A 4dsj_A 4dsk_A 4dsl_A 4e0d_A 4ez6_D 4ez9_A 4f2r_D 4f2s_D 4f3o_A 4f4k_D 4f8r_A 4uqg_A 6dsu_A 6dsv_A 6dsw_A 6dsx_A 6dsy_A 6mu4_A 6mu5_A 6p5c_A 6ueu_A 6ur2_A 6ur4_A 6ur9_A 6us5_A 7k5o_A 7k5p_A 7k5q_A 7k5r_A 7k5s_A 7k5t_A 7k5u_A
links to other resources	NAKB PDIdb DNAproDB
protein sequence	> 4yfu_D interface=285,290,318,325,328,332,361,417,496,500,532, kkmaftladrvteemladkaalvvevveenyhdapivgiavvnehgrfflrpetaladpqfvawlgdetkkksmfdskraavalkwkgielgvsfdlllaaylldpaqgvddvaaaakmkqyeavrpdeavygkgakravpdepvlaehlvrkaaaiwelerpfldelrrneqdrllveleqplssilaemefagvkvdtkrleqmgkelaeqlgtveqriyelagqefninspkqlgvilfeklqlpvlkktktgystsadvleklapyheivenilhyrqlgKlqstYiegllkvvrpatkkvhtifnqaltqtgRlsstepNlqNipiRleegrkirqafvpsesdwlifaadysqiElrvlahiaeddnlmeafrrdldihtktamdifqvsedevtpnmrrqakavnygivYgisdyglaqnlnisrkeaaefieryfesfpgvkrymenivqeakqkgyvttllhrrrylpditsrnfnvrsfaermamNtpiQgsaadiikkamidlnarlkeerlqahlllqvHdelileapkeemerlcrlvpevmeqavtlrvplkvdyhygstwydak

No structural evidence for specific binding to DNA (<4 informative columns)

Dendrogram of similar interfaces ?

matrix format

  
  --------------------------------KT------YG------RGNGNGRC----YG--YAIGSCYC----NG--RC--------FG--------QAHG                                          +-4yfu_D    
                                                                                                                                                  +-2 
  ----------------------------------RC------------RANGNGRT----YG--YT--SCYC--------------------------NTQT--   L                                    ! ! +-6vdd_A    
                                                                                                                                           +------4 +-1 
  LCNGKGYGMG--RCFCEC----EG------------------SGHGVC--------------------------------------------------------                                 !      !   +-1kln_A    
                                                                                                                                           !      ! 
  --------------------------------NA----KG--------RC--NT----QC----------------------------NG--YGATRT--QGHC                               +-6      +---4x0p_B    
                                                                                                                                         ! ! 
  ------------------------IAAAVAAAKC--------------RTNGNC----TC----YCMCSAHARAQAEA--------------------NGQG--                               ! !       +--6fbc_A    
                                                                                                                                    +----7 +-------3 
  --------------------------------------------------NANC------FC--YG------RG----------------------RGNGQC--   L                      !    !         +--1tau_A    
                                                                                                                                    !    ! 
  --------------------------------KT--------------RG------EGKGYGACYCAC----RC------------------QTATRTNGQGHC   L           +----------8    !    +-------4xvk_A    
                                                                                                                         !          !    +----5 
  ------------------------------------KA--------------NT----------------------------------------------QGHT   L           !          !         +-------6xbu_A    
                                                                                                                       +-9          ! 
  --------------------------------------KT--------RTNG------------YA----------------------------------QA--             ! !          +-----------------1x9m_A    
                                                                                                                    +-10 ! 
  ----------DA--------FA----------------------------------------------------------------------------------          !  ! +----------------------------3qex_A    
                                                                                                                 +-11  !  
  ------------------------------------------------------------------------------SGRGPTSGRG----------------   L   !  !  +----------------------------7bhy_A    
                                                                                                               -12  !  
  ------------------------------------------------------------------------------------------------RG------   L   !  +-----------------------------6ymv_A    
                                                                                                                 !  
  TT----------------HT------------------------------------------------------------------------------------       +-----------------------------2py5_B

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updated Tue Dec 19 09:46:41 2023