› 5nw9

X-ray diffraction
2.04Å resolution

Crystal structure of the complex of Tdp1 with duplex DNA

Released:
DOI: 10.2210/pdb5nw9/pdb
PDB entry 5nw9 coloured by chain, front view.
PDB entry 5nw9 coloured by chain, side view.
PDB entry 5nw9 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1.
Flett FJ, Ruksenaite E, Armstrong LA, Bharati S, Carloni R, Morris ER, Mackay CL, Interthal H, Richardson JM
OpenAccess logo Nat Commun 9 24 (2018)
PMID: 29295983

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-509743 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Tyrosyl-DNA phosphodiesterase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 485 amino acids
Theoretical weight: 54.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NUW8 (Residues: 149-608; Coverage: 76%)
Gene name: TDP1
Sequence domains: Tyrosyl-DNA phosphodiesterase
Structure domains: Endonuclease Chain A
DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21212
Unit cell:
a: 108.01Å b: 195.31Å c: 50.83Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.232 0.271
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC).
Sun et al. (2020)
4 more

2 mentions without citation

Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1.
Flett et al. (2018)
1 more