1K4T: Human DNA topoisomerase I

Human DNA topoisomerase I (70 kda) in complex with the poison topotecan and covalent complex with a 22 base pair DNA duplex. Determined by X-ray diffraction at 2.1 Å resolution. Released 4 Dec 2002.

Method
X-ray diffraction
Resolution
2.1 Å
Organism
Homo sapiens
Chains
4
Atoms
5,883
Mol. weight
84.97 kDa
Ligands
TTG, TTC, HG
Released
4 Dec 2002

Explore 1K4T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1K4T contains 34 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: 34 helices, 23 β-strands

ElementResiduesLengthSheet
α-helix205-2073
α-helix211-2122
β-strand220-22231
β-strand22612
α-helix227-2315
α-helix233-2353
β-strand241-24223
β-strand245-24623
α-helix248-2503
α-helix251-26212
α-helix267-2704
α-helix272-28514
α-helix288-2936
β-strand300-30123
α-helix303-31614
α-helix321-33818
β-strand340-34341
β-strand346-34941
β-strand35014
β-strand35412
α-helix355-3584
β-strand359-36025
β-strand373-37425
α-helix375-3773
α-helix379-3813
β-strand383-38536
α-helix391-3955
β-strand403-40536
β-strand414-41746
α-helix4231
β-strand424-42746
β-strand42914
α-helix434-45118
α-helix454-46411
α-helix470-48415
α-helix504-5063
β-strand50817
α-helix509-5113
β-strand512-51878
β-strand521-530108
α-helix532-5343
β-strand536-54278
α-helix545-55410
β-strand56317
α-helix570-58011
α-helix588-60518
α-helix612-62918
β-strand63319
α-helix640-6434
α-helix644-67330
α-helix678-71033
β-strand71419
α-helix717-7226
α-helix726-73611
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
>1K4T_1 5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*T)-3' (chains B)
AAAAAGACTT
Sequence of entity 2 (C), FASTA
>1K4T_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
>1K4T_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
>1K4T_4 DNA topoisomerase I (chains A)
KKPKNKDKDKKVPEPDNKKKKPKKEEEQKWKWWEEERYPEGIKWKFLEHKGPVFAPPYEP
LPENVKFYYDGKVMKLSPKAEEVATFFAKMLDHEYTTKEIFRKNFFKDWRKEMTNEEKNI
ITNLSKCDFTQMSQYFKAQTEARKQMSKEEKLKIKEENEKLLKEYGFCIMDNHKERIANF
KIEPPGLFRGRGNHPKMGMLKRRIMPEDIIINCSKDAKVPSPPPGHKWKEVRHDNKVTWL
VSWTENIQGSIKYIMLNPSSRIKGEKDWQKYETARRLKKCVDKIRNQYREDWKSKEMKVR
QRAVALYFIDKLALRAGNEKEEGETADTVGCCSLRVEHINLHPELDGQEYVVEFDFLGKD
SIRYYNKVPVEKRVFKNLQLFMENKQPEDDLFDRLNTGILNKHLQDLMEGLTAKVFRTYN
ASITLQQQLKELTAPDENIPAKILSYNRANRAVAILCNHQRAPPKTFEKSMMNLQTKIDA
KKEQLADARRDLKSAKADAKVMKDAKTKKVVESKKKAVQRLEEQLMKLEVQATDREENKQ
IALGTSKLNYLDPRITVAWCKKWGVPIEKIYNKTQREKFAWAIDMADEDYEF

Ligands and cofactors

IDNameFormulaCopies
TTG2-(1-dimethylaminomethyl-2-hydroxy-8-hydroxymethyl-9-oxo-9,11-dihydro-indolizin…C23 H25 N3 O61
TTC(s)-10-[(dimethylamino)methyl]-4-ethyl-4,9-dihydroxy-1H-PYRANO[3',4':6,7]INOLIZ…C23 H23 N3 O51
HGMercury (II) ionHg1

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

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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