triangle PDBeMotif: 1k4t  
  coner Sequences coner   coner 3D motifs coner   coner Ligand environment coner   coner Ligand bonds coner
   
coner
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Enzyme   5.99.1.2
Classification isomerase/dna    | release date: Mon, Oct 8, 2001
Title human dna topoisomerase i (70 kda) in complex with the poison topotecan and covalent complex with a 22 base pair dna duplex
Authors A.B.BURGIN JR., B.L.STAKER, C.A.BEHNKE, K.HJERRILD, L.J.STEWART, M.D.FEESE
Method X-RAY DIFFRACTION (resolution: 2.10Å)
PDBe Citation   
Small molecules:    search TTC TTC binding statistics TTC   search HG HG binding statistics HG   search PG4 PG4 binding statistics PG4   search TTG TTG binding statistics TTG
Modified residues:  search TGP TGP binding statistics TGP search PTR PTR binding statistics PTR
Ligand bond colours:   *  covalent   *  ionic   *  hydrogen   *  electrostatic   *  van-der-waals   *  plane-atom   *  plane-plane   *  undefined  - Click here to show 5Å bonds
Chain A sequence:
KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKA
EEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEK
LLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWL
VSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEK
EEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGIL
NKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDA
KKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWC
KKWGVPIEKIYNKTQREKFAWAIDMADEDYEF
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 TOPOISOMERASE I
member of: CATH:search1.10.10.41/search1.10.132.10/search2.170.11.10/search3.90.15.10GENE3D:searchG3DSA_1.10.10.41/searchG3DSA_1.10.132.10/searchG3DSA_2.170.11.10/searchG3DSA_3.90.15.10PANTHER:searchPTHR10290/searchPTHR10290_SF1PFAM:searchPF01028/searchPF02919/searchPF14370PRINTS:searchEUTPISMRASEIPROSITE PATTERNS:searchPS00176, SMART:searchSM00435SUPERFAMILY:searchSSF46596/searchSSF56349/searchSSF56741UniProt:searchP11387
JMol viewer RasMol script viewer  PG4 901A  ..                                                                                                                                                                                                                                                                                                           *         **                  *                                                                                                                                                                                                                                           
JMol viewer RasMol script viewer  HG 900A  ..                                                                                                                                                                                                                                                                                                           |         ||                  |                                                                                                   *                                                                                                                                       
JMol viewer RasMol script viewer  TTC 990D  ..                                                                                                                                                                   *                                                                                                                                       |         ||                  | **                                                                                                |                                                                                       *                                               
JMol viewer RasMol script viewer  TTG 991D  ..                                                                                                                                                                   *                                                                                                                                       |         ||                  | **                                                                                                |                                                                                       *   *                                           
sec str:  .....hhhhh...........ee...................ee..ee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhheeee..eeee.........ee............ee...hhhh.eee.................eee........eeee......eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.................hhhhhhhh.eeeeeee..eeeeeeeeee.hhh.eeeeeee.hhhhhhhhhhhh.............hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.hhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhh.......
sequence :  ..QKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF
seq num:  ..201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761  
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  MYRISTYL ..    |  |                          |  |   |  |                 |  | |  |           |  ||   |    ||| |        |   |  |  |                 |  |           | |    ^*****  | || |     || ||    |  |     |  |       |  | |        | |      |  |   |                          |  | |               | ||| |    | |     |  ||| ||     |  |         |  |                  | || ||  |  |  |       | ||||  |  |  || |   |    ||  ||  |                   | |      | || ||                               | | |                            ||  |       |||| ||       | ||||||||   |          |  |  
search RasMol script viewer Motif-ligand binding stats  TOPOISOMERASE_I_EUK ..    |  |                          |  |   |  |                 |  | |  |           |  ||   |    ||| |        |   |  |  |                 |  |           | |            | || |     || ||    |  |     |  |       |  | |        | |      |  |   |                          |  | |               | ||| |    | |     |  ||| ||     |  |         |  |                  | || ||  |  |  |       | ||||  |  |  || |   |    ||  ||  |                   | |      | || ||                               | | |                            *************^*****       | ||||||||   |          |  |  
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  asxturn ..    |  |                          |  |   |  |                 |  | |  |           |  ||   |    *** |        |   |  |  |                 |  |           | |            | || |     || ||    |  |     |  |       |  | |        | |      |  |   |                          |  | |               | ||| |    | |     |  ||| ||     |  |         |  |                  | || ||  |  |  |       | || |  |  |  || |   |    ||  ||  |                   | |      | || ||                               ***                               |  |       | |***        | |||||||               |  |  
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  Catalytic site ..                                                                                                                                                                                                                                                                                               *                                                                                                     *                                         *                                                                                                                                     

chain B : 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'
JMol viewer RasMol script viewer  TTC 990D  ..         *
JMol viewer RasMol script viewer  TTG 991D  ..         *
sec str:  ............
sequence :  ..AAAAAGACTT
seq num:  ..1         

chain C : 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'
JMol viewer RasMol script viewer  TTC 990D  ..*           
JMol viewer RasMol script viewer  TTG 991D  ..*           
sec str:  ..............
sequence :  ..GGAAAAATTTTT
seq num:  ..11          

chain D : 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*CP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3';
JMol viewer RasMol script viewer  TTC 990D  ..           **         
JMol viewer RasMol script viewer  TTG 991D  ..           **         
sec str:  ........................
sequence :  ..AAAAATTTTTCCAAGTCTTTTT
seq num:  ..101       111         

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