1K4T

HUMAN DNA TOPOISOMERASE I (70 KDA) IN COMPLEX WITH THE POISON TOPOTECAN AND COVALENT COMPLEX WITH A 22 BASE PAIR DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The mechanism of topoisomerase I poisoning by a camptothecin analog

Staker, B.L.Hjerrild, K.Feese, M.D.Behnke, C.A.Burgin Jr., A.B.Stewart, L.J.

(2002) Proc Natl Acad Sci U S A 99: 15387-15392

  • DOI: 10.1073/pnas.242259599
  • Primary Citation of Related Structures:  
    1K4T, 1K4S

  • PubMed Abstract: 
  • We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by interca ...

    We report the x-ray crystal structure of human topoisomerase I covalently joined to double-stranded DNA and bound to the clinically approved anticancer agent Topotecan. Topotecan mimics a DNA base pair and binds at the site of DNA cleavage by intercalating between the upstream (-1) and downstream (+1) base pairs. Intercalation displaces the downstream DNA, thus preventing religation of the cleaved strand. By specifically binding to the enzyme-substrate complex, Topotecan acts as an uncompetitive inhibitor. The structure can explain several of the known structure-activity relationships of the camptothecin family of anticancer drugs and suggests that there are at least two classes of mutations that can produce a drug-resistant enzyme. The first class includes changes to residues that contribute to direct interactions with the drug, whereas a second class would alter interactions with the DNA and thereby destabilize the drug-binding site.


    Organizational Affiliation

    deCODE genetics, Incorporated, BioStructures Group, 7869 Northeast Day Road West, Bainbridge Island, WA 98110, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase IA592Homo sapiensMutation(s): 1 
Gene Names: TOP1
EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
Find proteins for P11387 (Homo sapiens)
Explore P11387 
Go to UniProtKB:  P11387
NIH Common Fund Data Resources
PHAROS  P11387
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3'B10N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3'C12N/A
      Find similar nucleic acids by: 
      (by identity cutoff)  |  Structure
      Entity ID: 3
      MoleculeChainsLengthOrganismImage
      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'D22N/A
      Small Molecules
      Ligands 4 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      TTG
      Query on TTG

      Download CCD File 
      C
      2-(1-DIMETHYLAMINOMETHYL-2-HYDROXY-8-HYDROXYMETHYL-9-OXO-9,11-DIHYDRO-INDOLIZINO[1,2-B]QUINOLIN-7-YL)-2-HYDROXY-BUTYRIC ACID
      C23 H25 N3 O6
      DPQJTQJZJNYUEC-QHCPKHFHSA-N
       Ligand Interaction
      TTC
      Query on TTC

      Download CCD File 
      D
      (S)-10-[(DIMETHYLAMINO)METHYL]-4-ETHYL-4,9-DIHYDROXY-1H-PYRANO[3',4':6,7]INOLIZINO[1,2-B]-QUINOLINE-3,14(4H,12H)-DIONE
      C23 H23 N3 O5
      UCFGDBYHRUNTLO-QHCPKHFHSA-N
       Ligand Interaction
      HG
      Query on HG

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      A
      MERCURY (II) ION
      Hg
      BQPIGGFYSBELGY-UHFFFAOYSA-N
       Ligand Interaction
      PG4
      Query on PG4

      Download CCD File 
      A
      TETRAETHYLENE GLYCOL
      C8 H18 O5
      UWHCKJMYHZGTIT-UHFFFAOYSA-N
       Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      PTR
      Query on PTR
      AL-PEPTIDE LINKINGC9 H12 N O6 PTYR
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      TTCIC50:  9650   nM  BindingDB
      TTCIC50:  1080   nM  BindingDB
      TTCIC50:  1100   nM  BindingDB
      TTCIC50:  1028   nM  BindingDB
      TTCKd:  26.5   nM  BindingDB
      TTCEC50:  71.30000305175781   nM  BindingDB
      TTCIC50:  1000   nM  BindingDB
      TTCIC50:  20000   nM  BindingDB
      TTCIC50:  50   nM  BindingDB
      TTCIC50:  5550   nM  BindingDB
      TTCEC50:  54   nM  BindingDB
      TTCIC50:  5250   nM  BindingDB
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.10 Å
      • R-Value Free: 0.269 
      • R-Value Work: 0.229 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 57.093α = 90
      b = 116.26β = 94.16
      c = 75.217γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      CNXrefinement
      CNXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2002-12-04
        Type: Initial release
      • Version 1.1: 2008-04-27
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance