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Classification transcription    | release date: Tue, Nov 26, 2013
Title crystal structure of the n-terminal domain of the pa subunit of dhori virus polymerase
Authors D.BOUVIER, D.GUILLIGAY, G.KOCHS, J.KADLEC, R.W.H.RUIGROK, S.CUSACK, T.CREPIN, T.LUNARDI
Method X-RAY DIFFRACTION (resolution: 1.30Å)
PDBe Citation   
Small molecules:    search GOL GOL binding statistics GOL
Modified residues:  search CME CME binding statistics CME
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:
GAMDRHKPKSISSEIWALSETSKEWMSNLRPLEARIVECIKYTVCCHISDMHLHNGVPRYIVNMWTPPEVADQEMKRQNL
IFARPNVPDLLDLKERKGVYVKVYPDNGTPTDYQTAENEIFVRVSLSGQMSPITREYLDEVQRQDVTNFLVTIYNESLES
NLLERMQELYDTD
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 : POLYMERASE SUBUNIT PA
member of: PFAM:searchPF00603UniProt:searchD6PT85
JMol viewer RasMol script viewer  GOL 1168A  ..                                        *                   * * *                                                                                                       
sec str:  ...hhhhh....hhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhh..ee..ee.eee....hhhhhhhhhhhhh..........eee....eeeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..
sequence :  ..AMDRHKPKSISSEIWALSETSKEWMSNLRPLEARIVECIKYTVCCHISDMHLHNGVPRYIVNMWTPPEVADQEMKRQNLIFARPNVPDLLDLKERKGVYVKVYPDNGTPTDYQTAENEIFVRVSLSGQMSPITREYLDEVQRQDVTNFLVTIYNESLESNLLERMQEL
seq num:  ..0         10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160     
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION ..  |  ||  ||   |  | |||||  | |    |      |  | | || |         ||| |  |        | |   | |  || | || |           |  |   |  |     | ||| |   |   |   |   ||   || ^*** | |  || ||
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  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  nest ..  |  ||  ||   |  |  | ||  |                | | || |         ||| |           ***   | |        ***                  |  |       *** |   |       |   ||   ||   |  | |       
search RasMol script viewer Motif-ligand binding stats  niche ..  ********|   |  **** |****                | ******         *****                 ***                             ****           |   |       |   ||   ||   |  | |       
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 ..                    ***                                                                                                                                       ***       

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 : POLYMERASE SUBUNIT PA
member of: PFAM:searchPF00603UniProt:searchD6PT85
JMol viewer RasMol script viewer  GOL 1169B  ..                                                                                                                  ***                                                    
sec str:  ...hhhhh....hhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhh..ee..ee.eee....hhhhhhhhhhhhh..........eee....eeeeeeee..............eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh
sequence :  ..AMDRHKPKSISSEIWALSETSKEWMSNLRPLEARIVECIKYTVCCHISDMHLHNGVPRYIVNMWTPPEVADQEMKRQNLIFARPNVPDLLDLKERKGVYVKVYPDNGTPTDYQTAENEIFVRVSLSGQMSPITREYLDEVQRQDVTNFLVTIYNESLESNLLERMQELY
seq num:  ..0         10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160      
search RasMol script viewer Motif-ligand binding stats  ASN_GLYCOSYLATION .. || |||  ||   |  | |||||  | |    |      |  | | || |         ||| |  |     || ||| | | |  || | || |           |  |   |  |     | ||| |   |  ||   |   |       ^***|| |        
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  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  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 ..                    ***                                                                                                    ***                                ***        

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