1NH3: Human Topoisomerase I Ara-C Complex

Human Topoisomerase I Ara-C Complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 4 Mar 2003.

Method
X-ray diffraction
Resolution
3.1 Å
Organism
Homo sapiens
Chains
4
Atoms
4,394
Mol. weight
79.9 kDa
Released
4 Mar 2003

Explore 1NH3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NH3 contains 25 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: 25 helices, 23 β-strands

ElementResiduesLengthSheet
α-helix209-2113
β-strand221-22221
β-strand22612
α-helix232-2354
β-strand241-24223
β-strand245-24623
α-helix253-2619
α-helix272-2809
α-helix290-2934
α-helix297-2993
β-strand300-30123
α-helix303-31412
α-helix323-3264
α-helix333-3375
β-strand340-34231
β-strand348-34921
β-strand35014
β-strand35412
β-strand35915
β-strand37415
α-helix375-3784
β-strand383-38536
α-helix392-3954
β-strand403-40536
β-strand414-41746
β-strand424-42746
β-strand42914
α-helix434-44815
α-helix454-46310
α-helix464-4663
α-helix470-48415
β-strand49517
β-strand49817
β-strand50818
α-helix509-5113
β-strand512-51879
β-strand521-530109
α-helix5351
β-strand536-54279
α-helix545-55511
β-strand56318
α-helix570-58011
α-helix588-60417
α-helix616-6227
α-helix726-73510
α-helix740-7423
α-helix748-7514
α-helix753-7564

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
5'-d(*ap*ap*ap*ap*ap*gp*ap*cp*up*(ubb))-3'BDNA10
5'-d(*(gng)p*gp*ap*ap*ap*ap*ap*up*up*up*up*t)-3'CDNA12
5'-d(*ap*ap*ap*ap*ap*tp*up*up*up*up*cp*(car)p*ap*ap*gp*up*cp*up*up*up*up*t)-3'DNA-hybrid22
DNA topoisomerase IAprotein563Homo sapiensP11387 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>1NH3_1 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*UP*(UBB))-3' (chains B)
AAAAAGACUX
Sequence of entity 2 (C), FASTA
>1NH3_2 5'-D(*(GNG)P*GP*AP*AP*AP*AP*AP*UP*UP*UP*UP*T)-3' (chains C)
XGAAAAAUUUUT
Sequence of entity 3 (D), FASTA
>1NH3_3 5'-D(*AP*AP*AP*AP*AP*TP*UP*UP*UP*UP*CP*(CAR)P*AP*AP*GP*UP*CP*UP*UP*UP*UP*T)-3' (chains D)
AAAAATUUUUCCAAGUCUUUUT
Sequence of entity 4 (A), FASTA
>1NH3_4 DNA topoisomerase I (chains A)
WKWWEEERYPEGIKWKFLEHKGPVFAPPYEPLPENVKFYYDGKVMKLSPKAEEVATFFAK
MLDHEYTTKEIFRKNFFKDWRKEMTNEEKNIITNLSKCDFTQMSQYFKAQTEARKQMSKE
EKLKIKEENEKLLKEYGFCIMDNHKERIANFKIEPPGLFRGRGNHPKMGMLKRRIMPEDI
IINCSKDAKVPSPPPGHKWKEVRHDNKVTWLVSWTENIQGSIKYIMLNPSSRIKGEKDWQ
KYETARRLKKCVDKIRNQYREDWKSKEMKVRQRAVALYFIDKLALRAGNEKEEGETADTV
GCCSLRVEHINLHPELDGQEYVVEFDFLGKDSIRYYNKVPVEKRVFKNLQLFMENKQPED
DLFDRLNTGILNKHLQDLMEGLTAKVFRTYNASITLQQQLKELTAPDENIPAKILSYNRA
NRAVAILCNHQRAPPKTFEKSMMNLQTKIDAKKEQLADARRDLKSAKADAKVMKDAKTKK
VVESKKKAVQRLEEQLMKLEVQATDREENKQIALGTSKLNYLDPRITVAWCKKWGVPIEK
IYNKTQREKFAWAIDMADEDYEF

Primary citation

Structural Impact of the Leukemia Drug 1-beta-D-Arabinofuranosylcytosine (Ara-C) on the Covalent Human Topoisomerase I-DNA Complex. Chrencik, J.E., Burgin, A.B., Pommier, Y. et al. J Biol Chem (2003) 278:12461-12466. DOI 10.1074/jbc.M212930200 · PubMed

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

Browse structure collections

About this viewer

MolViewer shows 1NH3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.