5J3S: Tyrosyl-DNA phosphodiesterase 2

Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2 in complex with a small molecule inhibitor. Determined by X-ray diffraction at 3.4 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,761
Mol. weight: 29.21 kDa
Ligands: 6FQ
Released: 4 May 2016

Explore 5J3S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J3S contains 6 α-helices and 15 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: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	114-120	7	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	189-198	10	2
β-strand	207-215	9	2
β-strand	218	1	2
β-strand	221-226	6	2
α-helix	234-248	15
β-strand	258-262	5	2
α-helix	269-272	4
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	316-320	5	2
β-strand	329-335	7	1
α-helix	350	1
β-strand	351-356	6	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tyrosyl-DNA phosphodiesterase 2	A	protein	253	Homo sapiens	O95551 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5J3S_1 Tyrosyl-DNA phosphodiesterase 2 (chains A)
GSHMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYE
IITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLES
TRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRSGGLPNNIVDVWEFLGK
PKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPS
DHWGLLCNLDIIL

Ligands and cofactors

ID	Name	Formula	Copies
6FQ	2,4-dioxo-10-[3-(1H-tetrazol-5-yl)phenyl]-2,3,4,10-tetrahydropyrimido[4,5-b]qui…	C19 H10 N8 O2	1

Primary citation

Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2. Hornyak, P., Askwith, T., Walker, S. et al. Biochem J (2016) 473:1869-1879. DOI 10.1042/BCJ20160180 · 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
5INO 3.21 Å, Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex

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