1K4T Isomerase Dna date Oct 08, 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 B.L.Staker, K.Hjerrild, M.D.Feese, C.A.Behnke, A.B.Burgin Jr., L.J.Stewart
compound source
Molecule: 5'-D(Apapapapapgpapcptpt)-3'
Chain: B
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D((Tgp)Pgpapapapapaptptptptpt)-3'
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: 5'- D(Apapapapaptptptptptpcpcpapapgptpcptptp Tptpt)-3';
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Dna Topoisomerase I
Chain: A
Fragment: Core Domain And C-Terminal Domain, Residues 174- 765;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_vector_type: Baculovirus
Expression_system_vector: Pfactbac1
symmetry Space Group: P 1 21 1
R_factor 0.229 R_Free 0.269
length a length b length c angle alpha angle beta angle gamma
57.093 116.260 75.217 90.00 94.16 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand HG, PG4, PTR, TGP, TTC, TTG BindingDB enzyme Isomerase E.C. BRENDA
note 1K4T (Molecule of the Month:pdb160)
related structures by homologous chain: 1A31

Primary referenceThe mechanism of topoisomerase I poisoning by a camptothecin analog., Staker BL, Hjerrild K, Feese MD, Behnke CA, Burgin AB Jr, Stewart L, Proc Natl Acad Sci U S A 2002 Nov 26;99(24):15387-92. Epub 2002 Nov 8. PMID:12426403
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (125 Kb) [Save to disk]
  • Biological Unit Coordinates (1k4t.pdb1.gz) 120 Kb
  • LPC: Ligand-Protein Contacts for 1K4T
  • CSU: Contacts of Structural Units for 1K4T
  • Likely Quarternary Molecular Structure file(s) for 1K4T
  • Structure Factors (783 Kb)
  • Retrieve 1K4T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1K4T from S2C, [Save to disk]
  • Re-refined 1k4t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1K4T in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1K4T
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1K4T, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1k4ta3, region A:201-430 [Jmol] [rasmolscript] [script source]
        - Domain d1k4ta2, region A:431-640,A:713-765 [Jmol] [rasmolscript] [script source]
        - Domain d1k4ta1, region A:641-712 [Jmol] [rasmolscript] [script source]
  • Fold representative 1k4t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1k4t_C] [1k4t_A] [1k4t] [1k4t_B] [1k4t_D]
  • SWISS-PROT database: [P11387]
  • Domain organization of [TOP1_HUMAN] by SWISSPFAM
  • Domain found in 1K4T: [TOPEUc ] by SMART
  • Other resources with information on 1K4T
  • Community annotation for 1K4T at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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