5J3P: Tyrosyl-DNA phosphodiesterase 2

Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2. Determined by X-ray diffraction at 3.1 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,556
Mol. weight: 57.79 kDa
Ligands: MG
Released: 4 May 2016

Explore 5J3P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5J3P contains 11 α-helices and 30 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: 6 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	189-198	10	2
β-strand	207-215	9	2
β-strand	218-224	7	2
β-strand	226	1	2
α-helix	234-249	16
β-strand	256-262	7	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	316-321	6	2
β-strand	329-337	9	1
α-helix	352	1
β-strand	353-360	8	1

Chain B: 5 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	115-120	6	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	189-198	10	5
β-strand	207-215	9	5
β-strand	218-224	7	5
β-strand	226	1	5
α-helix	235-249	15
β-strand	256-262	7	5
β-strand	282	1	5
α-helix	283-286	4
β-strand	297-298	2	6
β-strand	312-313	2	6
β-strand	316-319	4	5
β-strand	329-337	9	4
α-helix	352	1
β-strand	353-360	8	4

Molecules and chains

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

Sequence of entity 1 (A, B), FASTA

>5J3P_1 Tyrosyl-DNA phosphodiesterase 2 (chains A, B)
GSHMFSLITWNIDGLDLNNLSERARGVCSYLALYSPDVIFLQEVIPPYYSYLKKRSSNYE
IITGHEEGYFTAIMLKKSRVKLKSQEIIPFPSTKMMRNLLCVHVNVSGNELCLMTSHLES
TRGHAAERMNQLKMVLKKMQEAPESATVIFAGDTNLRDREVTRSGGLPNNIVDVWEFLGK
PKHCQYTWDTQMNSNLGITAACKLRFDRIFFRAAAEEGHIIPRSLDLLGLEKLDCGRFPS
DHWGLLCNLDIIL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2

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

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
5INO 3.21 Å, Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex
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 5J3P 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.