triangle PDBeMotif: 1kfv  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
   Search  |  PDB header search  |  Upload PDB file  |  Molecule binding  |  Pair bonds  |  Motif binding  |  3D environment  |  Motif inclusion  
coner
AstexViewer TM
Download original PDB file
Download xml file
Download structure factors file
Enzyme   3.2.2.23
Classification hydrolase/dna    | release date: Fri, Nov 23, 2001
Title crystal structure of lactococcus lactis formamido-pyrimidine glycosylase (alias fpg or mutm) non covalently bound to an containing dna.
Authors B.CASTAING, C.ZELWER, K.PEREIRA DE JESUS, L.SERRE, S.BOITEUX
Method X-RAY DIFFRACTION (resolution: 2.55Å)
PDBe Citation   
Small molecules:    search ZN ZN binding statistics ZN   search GOL GOL binding statistics GOL
Modified residues:  search MSE MSE binding statistics MSE
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:
GELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQGISRRGKYLIFEIGDDFRLISHLRMEGKYR
LATLDAPREKHDHLTMKFADGQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYL
LEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSIRTYSALGSTGKMQNELQVYGK
TGEKCSRCGAEIQKIKVAGRGTHFCPVCQQK
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 : FORMAMIDO-PYRIMIDINE DNA GLYCOSYLASE
member of: CATH:search1.10.8.50/search3.20.190.10GENE3D:searchG3DSA_1.10.8.50/searchG3DSA_3.20.190.10HAMAP:searchMF_00103PANTHER:searchPTHR22993PFAM:searchPF01149/searchPF06827/searchPF06831PROSITE PATTERNS:searchPS01242, PROSITE PROFILES:searchPS51066/searchPS51068, SMART:searchSM00898SUPERFAMILY:searchSSF46946/searchSSF57716/searchSSF81624TIGRFAMS:searchTIGR00577UniProt:searchP42371
JMol viewer RasMol script viewer  GOL 301A  ..                                 *                       *               *                                      * *             *                                                                                          ..GOL ..                                             
JMol viewer RasMol script viewer  ZN 300A  ..                                 |                       |               |                                      | |             |                                                                                          ..ZN ..                  *  *                *  *   
sec str:  ...hhhhhhhhhhhhhhhhh...eeeeee.hhhhh..hhhhhhhhhh...eeeeeee..eeeeee...eeeeee.....eeeee.........eeeeeee...eeeee......eeeeee..hhhhhhhhh...........hhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh........ .....hhhhhh.................eeeee..eeeee.......
sequence :  ..GELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQGISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFADGQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGSSI... ..STGKMQNELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVCQQK
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211      ... ..227       237       247       257       267  
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..||     | |      |  |        ||||| |  |  || || |  || | ||||     |  |               |  |  |  |  | |         | ||||     |  |       |||    || |||   |   |**^*|       |||||  |        || ||||  ||| |||  || |   |  |       | | | ..PS00004.. | ||| ||  |||| | |  | |      |  ||   |  ||  
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..||     ^**      |  |        ||||| |  |  || |^**  || ^**|||     |  |               |  |  |  |  ^**         | ||||     |  |       |||    || |||   |   |  ^**       |||||  |        || ||||  ||| |||  || |   |  |       | | ^*..PS00005.. ^**|| ||  |||| | |  | |      |  ||   |  ||  
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..||              |  |        ||||| ^***  || || |  ||    |||     |  |               |  |  |  |              | ||||     |  |       |||    ^***||   |   |  | |       |||||  |        || ||||  ||| |||  || |   ^***       | |   ..PS00006..   ||| ||  |||| | |  | |      |  ||   |  ||  
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..||              |  |        |||||       || || |  ||    |||     |  |               |  |  |  |              | ||||     |  |       |*******^  ||   |   |  | |       |||||  |        || ||||  ||| |||  || |   |          | |   ..PS00007..   ********^||| | |  | |      |  ||   |  ||  
search RasMol script viewer Motif-ligand binding stats  ZF_FPG_1 ..||              |  |        |||||       || || |  ||    |||     |  |               |  |  |  |              | ||||     |  |       | |    |   ||   |   |  | |       |||||  |        || ||||  ||| |||  || |   |          | |   ..PS01242..    || ||   ||| | ^**^****************^**^*  
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..||              |  |        |||||       || || |  ||    |||     |  |               |  |  |  |              | ||||     |  |       | |    |   ||   |   |  | |       |||||  |        || ||||  ||| ||***** |   |          | |   ..alphabetamotif..    || ||   ||| |    | |      |  ||          
search RasMol script viewer Motif-ligand binding stats  asxmotif ..||              |  |        |||||       || || |  ||    |||     |  |               |  |  |  |              | ||||     |  |       | |    |   |*****   |  | |       |||||  |        || ||||  ||| |||  |  |   |          | |   ..asxmotif..    || ||   ||| |    | |      |  ||          
search RasMol script viewer Motif-ligand binding stats  betabulge ..||              |  |        |||||       || || |  **    |||     |  |               |  |  |  |              | ||||     |  |       | |    |   |        |  | |       |||||  |        || ||||  ||| |||  |  |   |          | |   ..betabulge..    || ||   ||| |    | |      |  ||          
search RasMol script viewer Motif-ligand binding stats  betaturn ..||              ****        *****       || ****        |||     |  |               ****  |  |              ****||     ****       | |    |   |        |  | |       |||||  |        |****|********|****  |   |          | |   ..betaturn..    ****|   |****    | |      ****|          
search RasMol script viewer Motif-ligand binding stats  nest ..||              |  |          | |       ||  |          |||     |  |               |  |  |  |                ****                ***    |   |        |  | |       ****|  |        |  ***|  | |  |      |   |          ***   ..nest..     |  |   *** |    ***          |          
search RasMol script viewer Motif-ligand binding stats  niche ..||              ****          ***       |****          ***     ****               ****  ****                 ***                       |   |        ******           ****        |    |**** ****      |   |                ..niche..     ****   *****                 |          
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..||                                      |   |           |                                                                              |   |           | |                       ******               |   |                ..schellmannloop..                                  |          
search RasMol script viewer Motif-ligand binding stats  stmotif ..||                                      |   |           |                                                                              *****           | |                                            |   |                ..stmotif..                                  |          
search RasMol script viewer Motif-ligand binding stats  ststaple ..||                                      *****           |                                                                                              | |                                            *****                ..ststaple..                                  |          
search RasMol script viewer Motif-ligand binding stats  stturn ..||                                                      |                                                                                              ***                                                                 ..stturn..                                  |          
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..**                                                      *                                                                                                                                                                  ..REP00000..                                  *          

chain D : 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-
JMol viewer RasMol script viewer  GOL 301A  ..        **   
sec str:  ...............
sequence :  ..CTCTTTPTTTCTC
seq num:  ..1         11 

chain E : 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
sec str:  ...............
sequence :  ..GAGAAACAAAGAG
seq num:  ..14        24 

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 : FORMAMIDO-PYRIMIDINE DNA GLYCOSYLASE
member of: CATH:search1.10.8.50/search3.20.190.10GENE3D:searchG3DSA_1.10.8.50/searchG3DSA_3.20.190.10HAMAP:searchMF_00103PANTHER:searchPTHR22993PFAM:searchPF01149/searchPF06827/searchPF06831PROSITE PATTERNS:searchPS01242, PROSITE PROFILES:searchPS51066/searchPS51068, SMART:searchSM00898SUPERFAMILY:searchSSF46946/searchSSF57716/searchSSF81624TIGRFAMS:searchTIGR00577UniProt:searchP42371
JMol viewer RasMol script viewer  GOL 302B  ..                                 *                       *               *                                      * *             *                                                                                        ..GOL ..                                           
JMol viewer RasMol script viewer  ZN 301B  ..                                 |                       |               |                                      | |             |                                                                                        ..ZN ..                * **                *  *   
sec str:  ...hhhhhhhhhhhhhhhhh..ee.eeee.hhhhh..hhhhhhhhhh.eeeeeeeee..eeeeee...eeeeee.....eeeee.........eeeeee....eeeee......eeeeee..hhhhhhhhh...........hhhhhhhhhhh...hhhhhhhh.......hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...... ...hhhhhh.................eeeee..eeeee.......
sequence :  ..GELPEVETVRRELEKRIVGQKIISIEATYPRMVLTGFEQLKKELTGKTIQGISRRGKYLIFEIGDDFRLISHLRMEGKYRLATLDAPREKHDHLTMKFADGQLIYADVRKFGTWELISTDQVLPYFLKKKIGPEPTYEDFDEKLFREKLRKSTKKIKPYLLEQTLVAGLGNIYVDEVLWLAKIHPEKETNQLIESSIHLLHDSIIEILQKAIKLGGS... ..GKMQNELQVYGKTGEKCSRCGAEIQKIKVAGRGTHFCPVCQQK
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201       211    ... ..229       239       249       259          
search RasMol script viewer Motif-ligand binding stats  CAMP_PHOSPHO_SITE ..||     | |      |  |         || | |  |  ||  | |  || | ||||     | |                |  |  |  |  | |         | ||||     |  ||  |   |||    || |||   |   |**^*|       |||||  |        || ||||  ||| |||  || |   |  |       | | ..PS00004.. ||| ||  |||| | |  | |      |  ||   || ||  
search RasMol script viewer Motif-ligand binding stats  PKC_PHOSPHO_SITE ..||     ^**      |  |         || | |  |  ||  ^**  || ^**|||     | |                |  |  |  |  ^**         | ||||     |  ||  |   |||    || |||   |   |  ^**       |||||  |        || ||||  ||| |||  || |   |  |       | | ..PS00005..**|| ||  |||| | |  | |      |  ||   || ||  
search RasMol script viewer Motif-ligand binding stats  CK2_PHOSPHO_SITE ..||              |  |         || | ^***  ||  |    ||    |||     | |                |  |  |  |              | ||||     |  ||  |   |||    ^***||   |   |  | |       |||||  |        || ||||  ||| |||  || |   ^***       | | ..PS00006.. ||| ||  |||| | |  | |      |  ||   || ||  
search RasMol script viewer Motif-ligand binding stats  TYR_PHOSPHO_SITE ..||              |  |         || |    |  ||  |    ||    |||     | |                |  |  |  |              | ||||     |  ||  |   |*******^  ||   |   |  | |       |||||  |        || ||||  ||| |||  || |   |          | | ..PS00007.. ********^||| | |  | |      |  ||   || ||  
search RasMol script viewer Motif-ligand binding stats  ZF_FPG_1 ..||              |  |         || |    |  ||  |    ||    |||     | |                |  |  |  |              | ||||     |  ||  |   | |    |   ||   |   |  | |       |||||  |        || ||||  ||| |||  || |   |          | | ..PS01242..  || ||   ||| | ^**^****************^**^*  
search RasMol script viewer Motif-ligand binding stats  alphabetamotif ..||              |  |         || |    *****  |    ||    |||     | |                |  |  |  |              | ||||     |  ||  |   | |    |   ||   |   |  | |       |||||  |        || ||||  ||| ||***** |   |          | | ..alphabetamotif..  || ||   ||| |    | |      |  ||    |  |  
search RasMol script viewer Motif-ligand binding stats  asxmotif ..||              |  |         || |    |  ||  |    ||    |||     | |                |  |  |  |              | ||||     |  ||  |   | |    |   |*****   |  | |       |||||  |        || ||||  ||| |||  |  |   |          | | ..asxmotif..  || ||   ||| |    | |      |  ||    |  |  
search RasMol script viewer Motif-ligand binding stats  asxturn ..||              |  |         || |    |  ||  |    ||    |||     | |                |  |  |  |              ***|||     |  ||  |   | |    |   |        |  | |       |||||  |        || ||||  ||| |||  |  |   |          | | ..asxturn..  || ||   ||| |    | |      |  ||    |  |  
search RasMol script viewer Motif-ligand binding stats  betabulge ..||              |  |         || |    |  ||  |    **    |||     | |                |  |  |  |                ||||     |  ||  |   | |    |   |        |  | |       |||||  |        || ||||  ||| |||  |  |   |          | | ..betabulge..  || ||   ||| |    | |      |  ||    |  |  
search RasMol script viewer Motif-ligand binding stats  betaturn ..||              ****         ****    ****|  |          |||     | |                ****  |  |                ||||     ********   | |    |   |        |  | |       |||||  |        |****|********|****  |   |          | | ..betaturn..  ****|   |****    | |      ****|    |  |  
search RasMol script viewer Motif-ligand binding stats  gammaturn ..||              |  |          | |       ||  |          |||     ***                |  |  |  |                ||||                | |    |   |        |  | |       |||||  |        |  | ||  | |  |      |   |          | | ..gammaturn..   |  |   ||| |    | |          |    |  |  
search RasMol script viewer Motif-ligand binding stats  nest ..||              |  |          | |       ||  |          |||                        |  |  |  |                ****                ***    |   |        |  | |       ****|  |        |  ***|  | |  |      |   |          *** ..nest..   |  |   *** |    ***          |    |  |  
search RasMol script viewer Motif-ligand binding stats  niche ..||              ****          ***       |****          ***                        ****  ****                 ***                       |   |        ******           ****        |    |**** ****      |   |              ..niche..   ****   *****                 |    ****  
search RasMol script viewer Motif-ligand binding stats  schellmannloop ..||                                      |   |           |                                                                              |   |           | |                       ******               |   |              ..schellmannloop..                                |          
search RasMol script viewer Motif-ligand binding stats  stmotif ..||                                      |   |           |                                                                              *****           | |                                            |   |              ..stmotif..                                |          
search RasMol script viewer Motif-ligand binding stats  ststaple ..||                                      *****           |                                                                                              | |                                            *****              ..ststaple..                                |          
search RasMol script viewer Motif-ligand binding stats  stturn ..||                                                      |                                                                                              ***                                                               ..stturn..                                |          
search RasMol script viewer Motif-ligand binding stats  Catalytic site ..**                                                      *                                                                                                                                                                ..REP00000..                                *          

chain G : 5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-
JMol viewer RasMol script viewer  GOL 302B  ..        **   
sec str:  ...............
sequence :  ..CTCTTTPTTTCTC
seq num:  ..1         11 

chain H : 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'
sec str:  ...............
sequence :  ..GAGAAACAAAGAG
seq num:  ..14        24 

   New search    1kfv:  Sequences  |  3D motifs  |  Ligand environment  |   Ligand bonds   |  SPICE view  |  PDB  |  XML  |  Structure factors