1SC7: Human DNA Topoisomerase I

Human DNA Topoisomerase I (70 Kda) In Complex With The Indenoisoquinoline MJ-II-38 and Covalent Complex With A 22 Base Pair DNA Duplex. Determined by X-ray diffraction at 3.0 Å resolution. Released 19 Apr 2005.

Method
X-ray diffraction
Resolution
3.0 Å
Organism
Homo sapiens
Chains
4
Atoms
5,629
Mol. weight
84.24 kDa
Ligands
M38
Released
19 Apr 2005

Explore 1SC7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1SC7 contains 33 α-helices and 23 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: 33 helices, 23 β-strands

ElementResiduesLengthSheet
α-helix209-2124
β-strand220-22231
β-strand22612
α-helix227-2315
β-strand240-24233
β-strand245-24733
α-helix251-26313
α-helix268-2703
α-helix272-28413
α-helix288-2936
α-helix297-2993
β-strand300-30123
α-helix305-31410
α-helix321-3244
α-helix327-33711
β-strand340-34341
β-strand346-34941
β-strand35014
β-strand35412
α-helix355-3584
β-strand36015
β-strand37315
α-helix376-3783
α-helix379-3813
β-strand383-38536
α-helix392-3954
β-strand403-40536
β-strand414-41746
α-helix4231
β-strand424-42746
β-strand42914
α-helix434-45118
α-helix454-46310
α-helix470-48415
β-strand49517
β-strand49817
β-strand50818
β-strand512-51549
β-strand524-53079
α-helix532-5343
β-strand536-54279
α-helix545-55511
β-strand56318
α-helix570-5789
α-helix588-60417
α-helix612-62514
α-helix648-6503
α-helix652-67423
α-helix682-6865
α-helix689-70113
α-helix703-7097
α-helix717-7226
α-helix726-7338
α-helix740-7423
α-helix746-7516
α-helix753-7575

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
5'-d(*ap*ap*ap*ap*ap*gp*ap*cp*tp*t)-3'BDNA10
5'-d(*(tgp)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*cp*ap*ap*gp*tp*cp*tp*tp*tp*tp*t)-3'DDNA22
DNA topoisomerase IAprotein592Homo sapiensP11387 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>1SC7_1 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' (chains B)
AAAAAGACTT
Sequence of entity 2 (C), FASTA
>1SC7_2 5'-D(*(TGP)P*GP*AP*AP*AP*AP*AP*TP*TP*TP*TP*T)-3' (chains C)
GGAAAAATTTTT
Sequence of entity 3 (D), FASTA
>1SC7_3 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' (chains D)
AAAAATTTTTCCAAGTCTTTTT
Sequence of entity 4 (A), FASTA
>1SC7_4 DNA topoisomerase I (chains A)
KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEP
LPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNI
ITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANF
KIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWL
VSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVR
QRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKD
SIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYN
ASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDA
KKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQ
IALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF

Ligands and cofactors

IDNameFormulaCopies
M384-(5,11-dioxo-5H-INDENO[1,2-c]isoquinolin-6(11H)-yl)butanoateC20 H15 N O41

Water and common crystallization additives (PG4) are not listed.

Primary citation

Structures of three classes of anticancer agents bound to the human topoisomerase I-DNA covalent complex. Staker, B.L., Feese, M.D., Cushman, M. et al. J Med Chem (2005) 48:2336-2345. DOI 10.1021/jm049146p · 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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