5INO: Tyrosyl-DNA phosphodiesterase 2

Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex. Determined by X-ray diffraction at 3.21 Å resolution. Released 27 Apr 2016.

Method: X-ray diffraction
Resolution: 3.21 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,373
Mol. weight: 64.19 kDa
Released: 27 Apr 2016

Explore 5INO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5INO contains 16 α-helices and 29 β-strands across 2 chains. 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: 8 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	113-120	8	1
α-helix	129-143	15
β-strand	147-153	7	1
α-helix	155-164	10
β-strand	168-172	5	1
β-strand	179-185	7	1
β-strand	190-198	9	2
β-strand	207-215	9	2
β-strand	218-224	7	2
β-strand	226	1	2
α-helix	227-229	3
α-helix	231-233	3
α-helix	234-250	17
β-strand	256-262	7	2
α-helix	267-272	6
β-strand	281-282	2	2
α-helix	283-286	4
β-strand	297-298	2	3
β-strand	312-313	2	3
β-strand	316-321	6	2
β-strand	329-337	9	1
α-helix	352	1
β-strand	353-360	8	1

Chain B: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	114-120	7	4
α-helix	129-143	15
β-strand	147-153	7	4
α-helix	155-164	10
β-strand	168-172	5	4
β-strand	179-185	7	4
β-strand	190-198	9	5
β-strand	207-215	9	5
β-strand	218-226	9	5
α-helix	227-229	3
α-helix	231-233	3
α-helix	234-250	17
β-strand	256-262	7	5
α-helix	267-272	6
β-strand	281-282	2	5
α-helix	283-286	4
β-strand	297-298	2	6
β-strand	312-313	2	6
β-strand	316-321	6	5
β-strand	330-337	8	4
α-helix	352	1
β-strand	353-359	7	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosyl-DNA phosphodiesterase 2	A, B	protein	258	Homo sapiens	O95551 (AlphaFold model)
DNA (5'-d(pcpcpgpapaptptpcp*g)-3')	C, D	DNA	9	Homo sapiens

Sequence of entity 1 (A, B), FASTA

>5INO_1 Tyrosyl-DNA phosphodiesterase 2 (chains A, B)
SNGQENGSMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKR
SSNYEIITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMT
SHLESTRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRCGGLPNNIVDVW
EFLGKPKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDC
GRFPSDHWGLLCNLDIIL

Sequence of entity 2 (C, D), FASTA

>5INO_2 DNA (5'-D(P*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') (chains C, D)
CCGAATTCG

Primary citation

Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2. Schellenberg, M.J., Perera, L., Strom, C.N. et al. Nucleic Acids Res (2016) 44:3829-3844. DOI 10.1093/nar/gkw228 · PubMed

Other PDB entries of the same protein (UniProt O95551 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q00 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 1
6Q01 0.85 Å, TDP2 UBA Domain Bound to Ubiquitin at 0.85 Angstroms Resolution, Crystal Form 2
5J3P 3.1 Å, Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2
5J3S 3.4 Å, Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in…

Browse structure collections

About this viewer

MolViewer shows 5INO 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.