triangle PDBeMotif: 1k3x  
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Enzyme   3.2.2.
Classification hydrolase/dna    | release date: Thu, Oct 4, 2001
Title crystal structure of a trapped reaction intermediate of the enzyme endonuclease viii with brominated-dna
Authors A.P.GROLLMAN, A.S.FERNANDES, D.O.ZHARKOV, G.GOLAN, G.SHOHAM, J.H.KYCIA, R.A.RIEGER, R.GILBOA, S.E.GER
Method X-RAY DIFFRACTION (resolution: 1.25Å)
PDBe Citation   
Small molecules:    search ZN ZN binding statistics ZN   search SO4 SO4 binding statistics SO4   search GOL GOL binding statistics GOL
Modified residues:  search BRU BRU binding statistics BRU
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTG
EEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQ
AFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRGQVDENKHHGALFRFKVFHRDGEPCERC
GSIIEKTTLSSRPFYWCPGCQH
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 : ENDONUCLEASE VIII
member of: CATH:search1.10.8.50/search3.20.190.10GENE3D:searchG3DSA_1.10.8.50/searchG3DSA_3.20.190.10HAMAP:searchMF_01253PANTHER:searchPTHR22993PFAM:searchPF01149/searchPF06827/searchPF06831PROSITE PATTERNS:searchPS01242, PROSITE PROFILES:searchPS51066/searchPS51068, SMART:searchSM00898SUPERFAMILY:searchSSF46946/searchSSF57716/searchSSF81624UniProt:searchP50465
JMol viewer RasMol script viewer  GOL 514A  ..                                                                                                                    **                                                                                               ..GOL ..                                        
JMol viewer RasMol script viewer  GOL 513A  ..                                                                                                                    ||                                                                                               ..GOL ..                                        
JMol viewer RasMol script viewer  GOL 512A  ..                                                                                                                    ||                                                                            *   *              ..GOL ..                                        
JMol viewer RasMol script viewer  GOL 511A  ..                                                                                                                    ||                            *   *                                           |   |              ..GOL ..                                        
JMol viewer RasMol script viewer  SO4 555A  ..                                                                                                                    ||                            |   |                                           |   |              ..SO4 ..                                        
JMol viewer RasMol script viewer  SO4 554A  ..*                                                                                                                   ||                            |   |                                           |   |              ..SO4 ..                                        
JMol viewer RasMol script viewer  SO4 553A  ..|                                                                                                                   ||                            |   |                                      **   |   |              ..SO4 ..                                        
JMol viewer RasMol script viewer  SO4 552A  ..|                                                                                                                   ||                     *      |   |                                      |*   |   |              ..SO4 ..                                        
JMol viewer RasMol script viewer  SO4 551A  ..|      *   *                                                                                                        ||                     |      |   |                                      ||   |   |              ..SO4 ..                                        
JMol viewer RasMol script viewer  ZN 501A  ..|      |   |                                                                                                        ||                     |      |   |                                      ||   |   |              ..ZN ..              *  *                *  *  
sec str:  ...hhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhhh...eeeeeee..eeeeee....eeeee.....eeeeee..........eeeeee...eeeeee...eeeee..hhhhhhhhhhhh.........hhhhhhhhhhh......hhhhhh.........hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... ........................eeeee..eeeee......
sequence :  ..PEGPEIRRAADNLEAAIKGKPLTDVWFAFPQLKTYQSQLIGQHVTHVETRGKALLTHFSNDLTLYSHNQLYGVWRVVDTGEEPQTTRVLRVKLQTADKTILLYSASDIEMLRPEQLTTHPFLQRVGPDVLDPNLTPEVVKERLLSPRFRNRQFAGLLLDQAFLAGLGNYLRVEILWQVGLTGNHKAKDLNAAQLDALAHALLEIPRFSYATRG... ..ALFRFKVFHRDGEPCERCGSIIEKTTLSSRPFYWCPGCQH
seq num:  ..1         11        21        31        41        51        61        71        81        91        101       111       121       131       141       151       161       171       181       191       201          ... ..223       233       243       253       
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  MYRISTYL ..||            | || |      | |  ||  ||  |^*****    |||      | |     || ||     |  |   | |  ||   |  |   |  | |    | ||| ||  |  |  | ||| ||   |  |  |  |  |    |  | | |  |        || |^***** |  |                        ..PS00008..    |  |||| | |  | |              || || 
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  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 B : 5'-D(*GP*GP*CP*(BRU)P*(BRU)P*CP*AP*(BRU)P*CP*CP*(P*GP*G)-3';
sec str:  ............
sequence :  ..CUUCAUCCUG
seq num:  ..403       

chain C : 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-
sec str:  ............
sequence :  ..CAGGAPGAAG
seq num:  ..422       

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