triangle PDBeMotif: 4f4w  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
AstexViewer TM
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Enzyme   2.7.7.7
Classification transferase/dna    | release date: Fri, May 11, 2012
Title y-family dna polymerase chimera dbh-dpo4-dpo4 #1
Authors J.D.PATA, R.C.WILSON
Method X-RAY DIFFRACTION (resolution: 1.90Å)
PDBe Citation   
Small molecules:    search DCP DCP binding statistics DCP   search CA CA binding statistics CA
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chains A,B sequence:
MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPI
YEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSK
PNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRT
RVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLL
QKILEEDERKIRRIGVRFSKFIEAIGLDKFFDTGGHHHHHH
Residue colours:  hydrophilic   hydrophobic   intermediate 
Assembly 1     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain A : DNA POLYMERASE IV
member of: CATH:search1.10.150.20/search3.30.1490.100/search3.30.70.270GENE3D:searchG3DSA_1.10.150.20/searchG3DSA_3.30.1490.100/searchG3DSA_3.30.70.270HAMAP:searchMF_01113PANTHER:searchPTHR11076/searchPTHR11076_SF12PFAM:searchPF00817/searchPF11798/searchPF11799PROSITE PROFILES:searchPS50173, SUPERFAMILY:searchSSF100879/searchSSF56672UniProt:searchQ4JB80/searchQ97W02
JMol viewer RasMol script viewer  CA 403A  ..      *                                                                                                 **                                                                                                                                                                                                                                            
JMol viewer RasMol script viewer  CA 402A  ..      **                                                                                                *|                                                                                                                                                                                                                                            
JMol viewer RasMol script viewer  DCP 401A  ..      |*****                               **  *  *     *                                               *|                                                     *                                                                                                                                                                                      
sec str:  ....eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.
sequence :  ..MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331         
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..         | |  ||   || || |       ||||  ||    ||   | ||||  |  || ||||  |          || ||| |  ||  |||    |  |   | |||||||   |  ||  |  |  | | |    |   || || | || ||  |         || |||| |  |  ||    ||  || |     |  ||  ||| ||||  |  || | ||||                | **^*||  || || ||||| ||| || |  ||        | |             |  ||| ||| | |||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..         | |  ||   || || |       ^**|  ||    ||   | ||||  |  || ||||  |          || ^** |  ||  |||    |  |   | ^**||||   |  ||  |  |  | | |    |   || || | || ||  |         || |||| |  |  ||    ||  || |     |  ||  ||| |^**  |  || | ||||                ^**   ||  || || ||||| ||| || |  ||        | |             |  ||| ^** | |||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..         | |  ||   || || |       ||||  ||    ||   | ||||  |  || ||||  |          || ||| |  ||  |||    ^***   | || ||||   |  ||  |  |  | | |    |   || || | || ||  |         || |||| |  |  ||    ||  || |     |  ||  ||| |||   |  || | ||||                      ||  || || ||||| ||| || |  ||        | |             |  ||| ||  | |||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..         | |  ||   || || |       ||||  ||    ||   | ||||  |  || ||||  |          || ||| |  ||  |||    |  |   | || ||||   |  ||  |  |  | | |    |   || || | || ||  |         || |||| |  |  ||    ||  || |     |  ||  ||| |||   |  || | ||||                      ********^ |*******^ || |  ||        | |             |  ||| ||  | |||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..         | |  ||   || || |       ||||  |^*****|   | |^*****  || ||||  |          || ||| |  ||  |||    |  |   | || ||^*****  ||  |  |  | | |    ^***** || | || ||  |         || |||| |  |  |^*****|  || |     |  ||  ||| |||   |  || | ||||                       |  || || ||||| ||| || |  ||        | |             |  ||| ||  | |||||| |     ^*****  
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..         | *****   || || |       ||||  |      |   | ||||  |  ******|  |          |***** |  ||  |||    |  |   | || ||||   *****  |  |  | | |        |  || | || ||  |         ******| |  |  |      ***** |     |  |**********   ***** | ||||                       ***** |**********| || |  ||        | |             *****| ||  | *****| |             
search RasMol script viewer Motif-ligand binding stats  asxmotif ..         | |  |    || || |       ||||  |      ***** ||||  |  || || |  |          || ||  |  ||  |||    |  |   | || |||*****  ||  |  |  | | |        ***** | || ||  |         || || | |  |  |      |  || |     |  ||  ||| ||    |  |  | ||||                       ***** || || |  ||| || |  ||        | |             |  ||| ||  | |||||| |             
search RasMol script viewer Motif-ligand binding stats  asxturn ..         | |  |    || || |       ||||  |          | ||||  |  || || |  |          || ||  |  ||  |||    |  |   ***| |||    |  ||  |  |  | | |           |  | || ||  |         || || | |  |  |      |  || |     |  ||  ||| ||    |  |  | ||||                       |  |  || || |  ||| || |  ||        | |             |  ||| ||  | |||||***             
search RasMol script viewer Motif-ligand binding stats  betabulge ..         | |  |    || || |       ||||  |          | ||||  |  || || |  |          || ||  |  ||  |**    |  |     || |||    |  ||  |  |  | | |           |  | || ||  |         || || | |  |  |      |  || |     |  ||  ||| ||    |  |  | ||||                       |  |  || || |  ||| || |  **        | |             |  ||| ||  | |||||| |             
search RasMol script viewer Motif-ligand binding stats  betaturn ..         | ****    ****| |       ||||  |          ****||  |  ***** |  |          *****  ****|  |      |  |     *****|    ********  **** | |           **** ****|  |         ***** | *******      ****| |     |  |*********    ******* ||||                       ****  *************** |            | |             ************ *****| |             
search RasMol script viewer Motif-ligand binding stats  nest ..         ***        | || |       ****  |            ***|  |        |  |                     |  |      |  |     |  ***                   ***                 |  |  |            |  | |  |  |          ***     |  |                     ****                                           | |            ***                            |  | |             
search RasMol script viewer Motif-ligand binding stats  niche ..                    ******          ****               ****        ****                     ****      ****     |    |                                       *******            **** *******                  ****                      ***                                           ***                                           ******             
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..                                                                                                               ******                                                                                                                                                                                                                                 

chain P : DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)
JMol viewer RasMol script viewer  CA 403A  ..            *
JMol viewer RasMol script viewer  DCP 401A  ..            *
sec str:  ...............
sequence :  ..GGCACTGATCGGC
seq num:  ..1         11 

chain T : DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'
JMol viewer RasMol script viewer  DCP 401A  .. *             
sec str:  .................
sequence :  ..CGGCCGATCAGTGCC
seq num:  ..4         14   

Assembly 2     View the assembly/model: ( JMolViewer Download PDB file RasMol script viewer AstexViewer™@MSD-EBI )
Motif search   chain:    Sequence numbers: 
   Using:   φ/ψ    residues code    secondary structures   
 coordinates of:  Cαs Side-chain
 
      View the fragment: rasmol script JMol viewer
chain B : DNA POLYMERASE IV
member of: CATH:search1.10.150.20/search3.30.1490.100/search3.30.70.270GENE3D:searchG3DSA_1.10.150.20/searchG3DSA_3.30.1490.100/searchG3DSA_3.30.70.270HAMAP:searchMF_01113PANTHER:searchPTHR11076/searchPTHR11076_SF12PFAM:searchPF00817/searchPF11798/searchPF11799PROSITE PROFILES:searchPS50173, SUPERFAMILY:searchSSF100879/searchSSF56672UniProt:searchQ4JB80/searchQ97W02
JMol viewer RasMol script viewer  CA 403B  ..      *                                                                                                 **                                                                                                                                                                                                                                            
JMol viewer RasMol script viewer  CA 402B  ..      **                                                                                                *|                                                                                                                                                                                                                                            
JMol viewer RasMol script viewer  DCP 401B  ..      ******                               **  *  *     *                                               *|                                                     *                                                                                                                                                                                      
sec str:  ....eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh...eeeeee..eeeee.hhhhh.hhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.
sequence :  ..MIVIFVDFDYFFAQVEEVLNPQYKGKPLVVCVYSGRTKTSGAVATANYEARKLGVKAGMPIIKAMQIAPSAIYVPMRKPIYEAFSNRIMNLLNKHADKIEVASIDEAYLDVTNKVEGNFENGIELARKIKQEILEKEKITVTVGVAPNKILAKIIADKSKPNGLGVIRPTEVQDFLNELDIDEIPGIGSVLARRLNELGIQKLRDILSKNYNELEKITGKAKALYLLKLAQDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFI
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331         
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..         | |       || || |       ||||  ||    ||   | ||||  |  || ||||  |          |  |||  |  |  |||    |  |   | ||||||    |  || |||||| | | |    |    | |  | || ||  |    |  |  |||||| |  |  ||    || ||| |     |  || |||| ||||  |  || | ||||                | **^*||  || || ||   | || || |  ||        | |                 || |||  ||||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..         | |       || || |       ^**|  ||    ||   | ||||  |  || ||||  |          |  ^**  |  |  |||    |  |   | ^**|||    |  || |||||| | | |    |    | |  | || ||  |    |  |  |||||| |  |  ||    || ||| |     |  || |||| |^**  |  || | ||||                ^**   ||  || || ||   | || || |  ||        | |                 || ^**  ||||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..         | |       || || |       ||||  ||    ||   | ||||  |  || ||||  |          |  ||   |  |  |||    ^***   | || |||    |  || |||||| | | |    |    | |  | || ||  |    |  |  |||||| |  |  ||    || ||| |     |  || |||| |||   |  || | ||||                      ||  || || ||   | || || |  ||        | |                 || |||  ||||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..         | |       || || |       ||||  ||    ||   | ||||  |  || ||||  |          |  ||   |  |  |||    |  |   | || |||    |  || |||||| | | |    |    | |  | || ||  |    |  |  |||||| |  |  ||    || ||| |     |  || |||| |||   |  || | ||||                      ********^ |*******^ || |  ||        | |                 || |||  ||||||| |     |    |  
search RasMol script viewer Motif-ligand binding stats  MYRISTYL ..         | |       || || |       ||||  |^*****|   | |^*****  || ||||  |          |  ||   |  |  |||    |  |   | || ||^*****  || |||||| | | |    ^***** |  | || ||  |    |  |  |||||| |  |  |^*****| ||| |     |  || |||| |||   |  || | ||||                       |  || |  ||   | || || |  ||        | |                 || |||  ||||||| |     ^*****  
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..         | |       || || |       ||||  |      |   | ||||  |  ******|  |          *****   |  |  |||    |  |   | || |||    ************ | | |           |  | || ||  |    |  ********| |  |  |     *****| |     |  |**********   ***** | ||||                       ***** *****   | || || |  ||        | |                 || |||  ||||||| |             
search RasMol script viewer Motif-ligand binding stats  asxmotif ..         | |       || || |       ||||  |      ***** ||||  |  || || |  |          |  |    |  |  |||    |  |   | || |||    |  || || ||  | | |           |  | || ||  |    |  |  | || | |  |  |     || ||| |     |  |*****| ||    |  |  | ||||                       ***** |  |    | || || |  ||        | |                 || |||  ||||||| |             
search RasMol script viewer Motif-ligand binding stats  asxturn ..         | |       || || |       ||||  |          | ||||  |  || || |  |          |  |    |  |  |||    |  |   ***| |||    |  || || ||  | | |           |  | || ||  |    |  |  | || | |  |  |     || ||| |     |  |***||| ||    |  |  | ||||                       |  |  |  |    | || || |  ||        | |                 || |||  ||||||***             
search RasMol script viewer Motif-ligand binding stats  betabulge ..         | |       || || |       ||||  |          | ||||  |  || || |  |          |  |    |  |  |**    |  |     || |||    |  || || ||  | | |           |  | || ||  |    |  |  | || | |  |  |     || ||| |     |  ||  ||| ||    |  |  | ||||                       |  |  |  |    | || || |  **        | |                 || |||  ||||||| |             
search RasMol script viewer Motif-ligand binding stats  betaturn ..         | |       ****| |       ||||  |          ****||  |  ***** |  |          ****    ****  |      |  |     *****|    ************** | |           **** ****|  |    ********** | *******     *****| |     |  |*********    ******* ||||                       ****  ****    ******| |            | |                 **************| |             
search RasMol script viewer Motif-ligand binding stats  nest ..         ***        | || |       ****  |            ***|  |        |  |                     |  |      |  |        ***                   ***                 |  |  |            |  | |  |  |          ***     |  |                     ****                                           | |            ***                            |  | |             
search RasMol script viewer Motif-ligand binding stats  niche ..                    ******          ****               ****        ****                     ****      ****                                                  *******            **** *******                  ****                      ***                                           ***                                           ******             

chain E : DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)
JMol viewer RasMol script viewer  CA 403B  ..            *
JMol viewer RasMol script viewer  DCP 401B  ..            *
sec str:  ...............
sequence :  ..GGCACTGATCGGC
seq num:  ..1         11 

chain F : DNA (5'-D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3'
JMol viewer RasMol script viewer  DCP 401B  .. *             
sec str:  .................
sequence :  ..CGGCCGATCAGTGCC
seq num:  ..4         14   

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