triangle PDBeMotif: 1xi1  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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coner
AstexViewer TM
Download original PDB file
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Download structure factors file
Enzyme   2.7.7.7
Classification transferase/dna    | release date: Tue, Sep 21, 2004
Title phi29 dna polymerase ssdna complex, monoclinic crystal form
Authors A.J.BERMAN, J.M.LAZARO, J.WANG, L.BLANCO, M.DE VEGA, M.SALAS, S.KAMTEKAR, T.A.STEITZ
Method X-RAY DIFFRACTION (resolution: 2.20Å)
PDBe Citation   
Small molecules:    search MG MG binding statistics MG
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:
MKHMPRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFK
WSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITP
EEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEK
EIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSG
GEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVT
GKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKL
GYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQ
VPGGVVLVDDTFTIK
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
member of: CATH:search1.10.287.690/search3.30.1770.10/search3.30.420.10/search3.90.1600.10/search4.10.80.20/search4.10.80.30GENE3D:searchG3DSA_1.10.287.690/searchG3DSA_3.30.1770.10/searchG3DSA_3.30.420.10/searchG3DSA_3.90.1600.10/searchG3DSA_4.10.80.20/searchG3DSA_4.10.80.30PFAM:searchPF03175PIRSF:searchPIRSF004178PRINTS:searchDNAPOLBPROSITE PATTERNS:searchPS00116, SMART:searchSM00486SUPERFAMILY:searchSSF53098/searchSSF56672UniProt:searchP03680
JMol viewer RasMol script viewer  MG 576A  ..                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
sec str:  .....eeeeeeee..hhhhh.eeeeeeee......eeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeee....eeeeeeee.hhh...hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....eee.hhhh..ee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee........ee.........ee........eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeee......ee.......eeeeeee....hhhhhh...........eeeeeeeeeee..eeeeeeeeee..
sequence :  ..PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK
seq num:  ..5         15        25        35        45        55        65        75        85        95        105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565        
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  DNA_POLYMERASE_B ..           | |  |   ||       | ||     |   |  |  || |     | |                     |  |     | |||                      |  ||    |  || | |      | |    |  |    |  ||                 | |   |   |    |  ||                   || ||       ||||| |           | |   |  |                |  | |           |  |                    | |       |   |   |  |               | |            |  |         |   |         | |        | |                  |   |    |   |     |  ||********* | |     |  || ||  |             |  |          | |                     | |     || |||  |                         
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..           | |  |   ||       | ||     |   |  ***** |     | |                     |  |     | |||                      *****    ***** | |      | |    |  |    *****                 | |   |   |    *****                   || ||       ||||| |           | |   |  |                |  | |           |  |                    | |       |   |   |  |               | |            |  |         |   |         | |        | |                  |   |    |   |     |  ||| | |     | |     |  || ||  |             |  |          | |                     | |     *****|  |                         
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  stmotif ..                                      *****                                                                                                                                             *****                                                                                                                                       *****                      | |                         |   |                                         |   |    |   |                                                                                          | |                                       
search RasMol script viewer Motif-ligand binding stats  ststaple ..                                                                                                                                                                                                                                                                                                                                                               | |                         *****                                         *****    *****                                                                                          | |                                       
search RasMol script viewer Motif-ligand binding stats  stturn ..                                                                                                                                                                                                                                                                                                                                                               ***                                                                                                                                                                               ***                                       

chain C : 5'-D(P*TP*TP*TP*TP*T)-3'
JMol viewer RasMol script viewer  MG 576A  ..   
sec str:  .....
sequence :  ..TTT
seq num:  ..3  

chain D : 5'-D(P*TP*TP*TP*TP*T)-3'
sec str:  .....
sequence :  ..TTT
seq num:  ..3  

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
member of: CATH:search1.10.287.690/search3.30.1770.10/search3.30.420.10/search3.90.1600.10/search4.10.80.20/search4.10.80.30GENE3D:searchG3DSA_1.10.287.690/searchG3DSA_3.30.1770.10/searchG3DSA_3.30.420.10/searchG3DSA_3.90.1600.10/searchG3DSA_4.10.80.20/searchG3DSA_4.10.80.30PFAM:searchPF03175PIRSF:searchPIRSF004178PRINTS:searchDNAPOLBPROSITE PATTERNS:searchPS00116, SMART:searchSM00486SUPERFAMILY:searchSSF53098/searchSSF56672UniProt:searchP03680
JMol viewer RasMol script viewer  MG 576B  ..                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
sec str:  .....eeeeeeee........eeeeeeee......eeee.hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeee....eeeeeeee.hhh...hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.....eee.hhhh..eeeeeeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee........ee.........ee........eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeeee..eeee.......eeeeeeee...hhhhhh...........eeeeeeeeee....eeeeeeeee..
sequence :  ..PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK
seq num:  ..5         15        25        35        45        55        65        75        85        95        105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565        
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 ..           | |  |   ||       | ||     |   |  |  || |     | |         |  |       ||  ||    | |||       || |  |        |  ||       || |||      ||| |  |  |********^              || |||   |   |    |  ||                   || ||       ||||| |           | |                   *******^||           |  |                   ||||   |   |   |   |  |               | |  ********^ |  |         |   |  |   |  | |        | |                  |   ||   |   |     |  ||| | |   |        || ||| ||  |   ||        |  |                              |  || |     ||||||  |                         
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