1K4S: DNA topoisomerase I

Human DNA topoisomerase I in covalent complex with a 22 base pair DNA duplex. Determined by X-ray diffraction at 3.2 Å resolution. Released 4 Dec 2002.

Method
X-ray diffraction
Resolution
3.2 Å
Organism
Homo sapiens
Chains
4
Atoms
4,858
Mol. weight
85.39 kDa
Released
4 Dec 2002

Explore 1K4S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K4S contains 25 α-helices and 24 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, 24 β-strands

ElementResiduesLengthSheet
α-helix205-2073
β-strand220-22121
β-strand22612
α-helix227-2315
α-helix233-2353
α-helix251-26111
α-helix267-2704
α-helix272-28413
α-helix288-2936
α-helix303-31614
α-helix321-33818
β-strand34013
β-strand342-34321
β-strand34611
β-strand34913
β-strand35014
β-strand35412
α-helix355-3584
β-strand36015
β-strand37315
α-helix379-3813
β-strand383-38536
β-strand38817
β-strand39017
α-helix392-3954
β-strand403-40536
β-strand414-41746
β-strand424-42746
β-strand42914
α-helix434-45017
α-helix455-46410
α-helix470-48516
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-helix586-60419
α-helix612-63019
α-helix719-7224
α-helix726-73611
α-helix740-7423
α-helix746-7516

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*(5IU)P*(5IU))-3'BDNA10
5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU)P*(5IU)P*(5IU)P*T)-3'CDNA12
5'-d(*ap*ap*ap*ap*ap*tp*(ido)up*(ido)up*(ido)up*(ido)up*cp*ap*ap*ap*gp*(ido)up*cp*(ido)up*(ido)up*(…DDNA22
DNA topoisomerase IAprotein592Homo sapiensP11387 (AlphaFold model)
Sequence of entity 1 (B), FASTA
>1K4S_1 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*(5IU)P*(5IU))-3' (chains B)
AAAAAGACUU
Sequence of entity 2 (C), FASTA
>1K4S_2 5'-D(*(SPT)P*GP*AP*AP*AP*AP*AP*(5IU)P*(5IU)P*(5IU)P*(5IU)P*T)-3' (chains C)
TGAAAAAUUUUT
Sequence of entity 3 (D), FASTA
>1K4S_3 5'-D(*AP*AP*AP*AP*AP*TP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*CP*AP*AP*AP*GP*(IDO)UP*CP*(IDO)UP*(IDO)UP*(IDO)UP*(IDO)UP*T)-3' (chains D)
AAAAATUUUUCAAAGUCUUUUT
Sequence of entity 4 (A), FASTA
>1K4S_4 DNA topoisomerase I (chains A)
KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEP
LPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNI
ITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANF
KIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWL
VSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVR
QRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKD
SIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYN
ASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDA
KKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQ
IALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF

Primary citation

The mechanism of topoisomerase I poisoning by a camptothecin analog. Staker, B.L., Hjerrild, K., Feese, M.D. et al. Proc Natl Acad Sci U S A (2002) 99:15387-15392. DOI 10.1073/pnas.242259599 · 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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