triangle PDBeMotif: 4elv  
  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: Wed, Apr 11, 2012
Title snapshot of the large fragment of dna polymerase i from ther aquaticus processing modified pyrimidines
Authors A.MARX, K.DIEDERICHS, S.OBEID
Method X-RAY DIFFRACTION (resolution: 1.90Å)
PDBe Citation   
Small molecules:    search MG MG binding statistics MG   search PGE PGE binding statistics PGE   search 0R7 0R7 binding statistics 0R7   search GOL GOL binding statistics GOL   search CA CA binding statistics CA   search EDO EDO binding statistics EDO
Modified residues:  search 0R8 0R8 binding statistics 0R8
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
ALEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDD
PMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLD
VAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKI
LQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYS
QIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAF
IERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRL
EEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
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 I, THERMOSTABLE
member of: GENE3D:searchG3DSA_1.10.150.20/searchG3DSA_1.20.1060.10/searchG3DSA_3.30.420.10/searchG3DSA_3.30.70.370PANTHER:searchPTHR10133/searchPTHR10133_SF20PFAM:searchPF00476/searchPF09281PRINTS:searchDNAPOLIPROSITE PATTERNS:searchPS00447, SMART:searchSM00482SUPERFAMILY:searchSSF53098/searchSSF56672TIGRFAMS:searchTIGR00593UniProt:searchP19821
JMol viewer RasMol script viewer  EDO 303C  ..                                                                                                                                                                                                                                                                                    *                                                                                                                                                             *                                                                                                        
JMol viewer RasMol script viewer  CA 908A  ..                                                                                                                                                                                                                                                                                    |                                       **                                                                                                                    |                                                        *                                               
JMol viewer RasMol script viewer  EDO 907A  ..                **                                                                                        *    *                                                                                                                                                                    |                                       ||                                                                                                                    |                                                        |                                               
JMol viewer RasMol script viewer  GOL 906A  ..                ||                                                                                        |    |                                              *                                                                                                                     |                         *  *          ||                                                                                                                    |                                                        |                                               
JMol viewer RasMol script viewer  GOL 905A  ..                ||                                                                                        |    |                   *                          |                                                                                                                     |                         |  |          ||                                                                                                               **   |                                                        |                         *                     
JMol viewer RasMol script viewer  PGE 904A  ..                ||                                                           *                            |    |           *       |     *   *                |                                                                                                                     |                         |  |          ||                                                                                                               ||   |                                                        |                         |                     
JMol viewer RasMol script viewer  GOL 903A  ..                ||                                                           |                            |    |           |       |     |   |                |                                                                                           **  *                     |        **  *            |  |          ||                                                                                                               ||   |                                                        |                         |                     
JMol viewer RasMol script viewer  0R7 902A  ..                ||                                                           |                            |    |           |       |     |   |                |                                                                                           ||  |                     |  *     ||  |            |  |          ******                       *                   **  **  *                                                       ||   |                                                        *                         |                     
JMol viewer RasMol script viewer  MG 901A  ..                ||                                                           |                            |    |           |       |     |   |                |                                                                                           ||  |                     |  |     ||  |            |  |          *|||||                       |                   ||  ||  |                                                       ||   |                                                        |*                        |                     
sec str:  ...eee........eeeeee.........eeeeeeee..eeee..hhhhhhh........hhhhhhhhhhhh........hhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh..................hhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhh.........eee.........eee..........hhhhhhhhh.ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheee.....eee.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeeeeee..hhhhhhhhhhhhhhh.........eeeeee.hhhhhh.
sequence :  ..LEEAPWPPPEGAFVGFVLSRKEPMWADLLALAAARGGRVHRAPEPYKALRDLKEARGLLAKDLSVLALREGLGLPPGDDPMLLAYLLDPSNTTPEGVARRYGGEWTEEAGERAALSERLFANLWGRLEGEERLLWLYREVERPLSAVLAHMEATGVRLDVAYLRALSLEVAEEIARLEAEVFRLAGHPFNLNSRDQLERVLFDELGLPAIGKTEKTGKRSTSAAVLEALREAHPIVEKILQYRELTKLKSTYIDPLPDLIHPRTGRLHTRFNQTATATGRLSSSDPNLQNIPVRTPLGQRIRRAFIAEEGWLLVALDYSQIELRVLAHLSGDENLIRVFQEGRDIHTETASWMFGVPREAVDPLMRRAAKTINFGVLYGMSAHRLSQELAIPYEEAQAFIERYFQSFPKVRAWIEKTLEEGRRRGYVETLFGRRRYVPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEGVYPLAVPLEVEVGIGEDWLSAKE
seq num:  ..294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824      
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..        | ||   |  ||||| ||  ||    |  |         || ||      | |     || ||||    |         |  ||| | |   |||  |||       | |      |  |            |   |    |   |                              | |  | |||  |       |||     | || |||||   |  |  |         |   |   ||  | || ||   | |     ^***  | | |  | ||| |   |   | || ||  |  |       || |   |   | ||  |    | |||  ||    | | |  |    |        |  | ||   |   | |               |  |      |  |  || |  | ||||    |  | | | ||         |   |  |            |  |||  || | |      |  ||       |      |              | |||||
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  AMIDATION ..        |  |       | || ||  ||    |  |         || ||      | |     || |||               |  | |   |   | |  | |                |  |            |   |    |   |                              | |  | |||  |       |||     |  ^***| |   |  |  |         |   |   |     || ||   | |           | |      ||| |   |   | || ||  |  |        | |   |   | |   |    | |||  ||    | | |  |    |           | ||   |   | |               |  |         ^***| |  | ^***    |  | |              |   |               |  |||  || | |      |  ||                             | | |  
search RasMol script viewer Motif-ligand binding stats  ATP_GTP_A ..        |  |       | || ||  ||    |  |         || ||      | |     || |||               |  | |   |   | |  | |                |  |            |   |    |   |                              | |  | |||  |       |********  | | | |   |  |  |         |   |   |     || ||   | |           | |      ||| |   |   | || ||  |  |        | |   |   | |   |    | |||  ||    | | |  |    |           | ||   |   | |               |  |             | |  | |||     |  | |              |   |               |  |||  || | |      |  ||                             | | |  
search RasMol script viewer Motif-ligand binding stats  DNA_POLYMERASE_A ..        |  |       | || ||  ||    |  |         || ||      | |     || |||               |  | |   |   | |  | |                |  |            |   |    |   |                              | |  | |||  |       | |        | | | |   |  |  |         |   |   |     || ||   | |           | |      ||| |   |   | || ||  |  |        | |   |   | |   |    | |||  ||    | | |  |    ********************   | |               |  |             | |  | |||     |  | |              |   |               |  |||  || | |      |  ||                             | | |  
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  betabulgeloop ..        |  |       | || ||        |  |         || ||      | |     || |||               |  | |   |   | |  | |                |  |            |   |    |   |                              | |  |  |   |       | |        | | | |   |  |  |         |   |   |     || ||   | |           | |       |  |   |   | || ||  |  |        | |   |   | |        | | |   |    | | |  |                | ||   |   | |               |  |             | |  *****     |  | |              |   |               |  | |     | |      |  |                                     
search RasMol script viewer Motif-ligand binding stats  betaturn ..        ****       | ****|        ****         ****|      | |     |****|               **** |   |   | |  | |                |  |            |   |    |   |                              | |  ****   |       | |        | | | |   *******         |   |   |     ****|   | |           | |       |  |   |   | ****|  ****        | |   |   | |        | | |   |    | | |  |                | ||   |   | |               ****             | |  ****|     **** |              |   |               **** |     | |      ****                                     
search RasMol script viewer Motif-ligand binding stats  gammaturn ..        |  |       | ||  |                      |  |      | |     |  | |                    |   |   | |  | |                |  |            |   |    |   |                              | |  |  |   |       | |        | | | |                   |   |   |      |  |   | |           | |       |  |   |   |  |  |  |  |        | |   |   | |        | | |   |    | | |  |                | ||   |   | |                                | |    | |     |  | |              |   |                  | |     ***                                               
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 ..                                                                  ******                    |   |        | |                                |   |    |   |                                      |   |                      | |                   |   |   |             | |                            |   |                          |   | |            |   |                               |   |                                                                         |   |                                                                            
search RasMol script viewer Motif-ligand binding stats  stmotif ..                                                                                            *****        | |                                |   |    |   |                                      *****                      | |                   |   |   |             | |                            *****                          |   | |            |   |                               *****                                                                         |   |                                                                            
search RasMol script viewer Motif-ligand binding stats  ststaple ..                                                                                                         | |                                *****    *****                                                                 | |                   *********             | |                                                           ***** |            *****                                                                                                             *****                                                                            
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                         ***                                                                                                               ***                                         ***                                                               ***                                                                                                                                                                                                               

chain B : DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(0R8)
JMol viewer RasMol script viewer  MG 201B  ..            
JMol viewer RasMol script viewer  0R7 902A  ..           *
JMol viewer RasMol script viewer  MG 901A  ..           |
sec str:  ..............
sequence :  ..GACCACGGCGCC
seq num:  ..101         

chain C : DNA (5'-D(*AP*AP*AP*GP*GP*GP*CP*GP*CP*CP*GP*TP*GP3');
JMol viewer RasMol script viewer  EDO 303C  ..  **         
JMol viewer RasMol script viewer  MG 302C  ..  ||         
JMol viewer RasMol script viewer  GOL 301C  .. **|         
JMol viewer RasMol script viewer  MG 201B  .. |||         
JMol viewer RasMol script viewer  GOL 903A  .. ||| **      
JMol viewer RasMol script viewer  0R7 902A  ..**|| ||      
sec str:  ...............
sequence :  ..GGGCGCCGTGGTC
seq num:  ..204          

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