triangle PDBeMotif: 2w9a  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
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Enzyme   2.7.7.7
Classification transferase/dna    | release date: Thu, Jan 22, 2009
Title ternary complex of dpo4 bound to n2,n2-dimethyl- deoxyguanosine modified dna with incoming dgtp
Authors C.J.RIZZO, F.P.GUENGERICH, H.ZHANG, I.D.KOSEKOV, M.EGLI, R.L.EOFF
Method X-RAY DIFFRACTION (resolution: 2.60Å)
PDBe Citation   
Small molecules:    search MG MG binding statistics MG   search DGT DGT binding statistics DGT
Modified residues:  search O2G O2G binding statistics O2G search DOC DOC binding statistics DOC
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
HHHHHHMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYL
PMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIA
ADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYN
EPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSE
SVKLLQKILEEDERKIRRIGVRFSKFIEAIGLDKFFDT
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: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:searchPTHR11076PFAM:searchPF00817/searchPF11798/searchPF11799PROSITE PROFILES:searchPS50173, SUPERFAMILY:searchSSF100879/searchSSF56672UniProt:searchQ97W02
JMol viewer RasMol script viewer  MG 1002A  ..                                                                                                                                                                                     *    *                                                                                                                                                            
JMol viewer RasMol script viewer  MG 1001A  ..       **                                                                                                *                                                                           |    |                                                                                                                                                            
JMol viewer RasMol script viewer  MG 1000A  ..       ||                                                                                                **                                                                          |    |                                                                                                                                                            
JMol viewer RasMol script viewer  DGT 594A  ..       ******                               **  *  *                        *                            *|                                                    *                     |    |                                                                                                                                                            
sec str:  .....eeeeee.hhhhhhhhhhhhhhh...eeeeee.......eeeeeehhhhhh.......hhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhh..eee....eeeee.hhhh.hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...eee.hhhhhhhhhhhh.hhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..
sequence :  ..HMIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIE
seq num:  ..0         10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330          
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  alphabetamotif ..          | |       || || |       ||||| |            | ||  |        |  |          |   |    |*****      | ||                             | |        |   |    |  |               |  ||| ||  |       || |||   |  |  *****  |          || ||||                       |   |               | |            | |            |   |           |  | |  ||          
search RasMol script viewer Motif-ligand binding stats  asxmotif ..          | |       || || |       ||||| |            | ||  |        |  |          |   |    || ||       | ||                             | |        *****    |  |               |  ||| ||  |       || |||   |  |  |  ||  |          || ||||                       *****               | |            | |            |   |           |  | |  ||          
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 ..                                                                                  |   |                | |                                                                                        ******                           ******                                                                          |   |                               
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 P : 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*DOC)-3';
JMol viewer RasMol script viewer  MG 1003A  ..             *
JMol viewer RasMol script viewer  MG 1002A  ..             |
JMol viewer RasMol script viewer  MG 1000A  ..             |
JMol viewer RasMol script viewer  DGT 594A  ..             *
sec str:  ................
sequence :  ..GGGGGAAGGATTCC
seq num:  ..1         11  

chain T : 5'-D(*TP*CP*AP*CP*O2GP*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3';
JMol viewer RasMol script viewer  DGT 594A  .. **             
sec str:  ..................
sequence :  ..ACGGAATCCTTCCCCC
seq num:  ..3         13    

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