1TL8: Human DNA topoisomerase I

Human DNA topoisomerase I (70 kDa) in complex with the indenoisoquinoline AI-III-52 and covalent complex with a 22 base pair DNA duplex. Determined by X-ray diffraction at 3.1 Å resolution. Released 21 Jun 2005.

Method
X-ray diffraction
Resolution
3.1 Å
Organism
Homo sapiens
Chains
4
Atoms
5,619
Mol. weight
84.04 kDa
Ligands
AI3
Released
21 Jun 2005

Explore 1TL8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TL8 contains 29 α-helices and 25 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 29 helices, 25 β-strands

ElementResiduesLengthSheet
β-strand220-22121
α-helix2251
β-strand22612
α-helix227-2315
α-helix233-2353
β-strand240-24233
β-strand245-24733
α-helix251-26313
α-helix267-2704
α-helix272-28413
α-helix288-2936
β-strand300-30123
α-helix303-31412
α-helix321-33717
β-strand340-34341
β-strand347-34931
β-strand35014
β-strand35412
α-helix355-3584
β-strand36015
β-strand37315
α-helix379-3813
β-strand382-38546
α-helix392-3965
β-strand403-40536
β-strand414-41746
β-strand424-42746
β-strand42914
α-helix434-45219
α-helix454-46310
α-helix470-48516
β-strand49517
β-strand49817
β-strand50818
α-helix509-5113
β-strand512-51879
β-strand521-52779
β-strand530110
α-helix532-5343
β-strand536110
β-strand539-54249
α-helix545-55511
β-strand56318
α-helix570-58011
α-helix588-60316
α-helix612-62918
α-helix651-66313
α-helix665-6684
α-helix689-70921
α-helix717-7215
α-helix726-73510
α-helix740-7423
α-helix746-7516
α-helix753-7586

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
5'-d(*ap*ap*ap*ap*ap*gp*ap*cp*tp*t)-3'BDNA10
5'-d(*(tpc)p*gp*ap*ap*ap*ap*ap*tp*tp*tp*tp*t)-3'CDNA12
5'-d(*ap*ap*ap*ap*ap*tp*tp*tp*tp*tp*cp*gp*ap*ap*gp*tp*cp*tp*tp*tp*tp*t)-3'DDNA22
DNA topoisomerase IAprotein592Homo sapiensP11387 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>1TL8_1 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' (chains B)
AAAAAGACTT
Sequence of entity 2 (C), FASTA
>1TL8_2 5'-D(*(TPC)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' (chains C)
CGAAAAATTTTT
Sequence of entity 3 (D), FASTA
>1TL8_3 5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*GP*TP*CP*TP*TP*TP*TP*T)-3' (chains D)
AAAAATTTTTCGAAGTCTTTTT
Sequence of entity 4 (A), FASTA
>1TL8_4 DNA topoisomerase I (chains A)
KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEP
LPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNI
ITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANF
KIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWL
VSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVR
QRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKD
SIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYN
ASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDA
KKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQ
IALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF

Ligands and cofactors

IDNameFormulaCopies
AI32,3-dimethoxy-12H-[1,3]DIOXOLO[5,6]INDENO[1,2-c]isoquinolin-6-iumC19 H16 N O41

Primary citation

Synthesis and Mechanism of Action Studies of a Series of Norindenoisoquinoline Topoisomerase I Poisons Reveal an Inhibitor with a Flipped Orientation in the Ternary DNA-Enzyme-Inhibitor Complex As Determined by X-ray Crystallographic Analysis. Ioanoviciu, A., Antony, S., Pommier, Y. et al. J Med Chem (2005) 48:4803-4814. DOI 10.1021/jm050076b · PubMed

Other PDB entries of the same protein (UniProt P11387 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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