› 8efg

X-ray diffraction
1.5Å resolution

Crystal structure of human TATDN1 bound to dAMP and two zinc ions

Released:
DOI: 10.2210/pdb8efg/pdb
PDB entry 8efg coloured by chain, front view.
PDB entry 8efg coloured by chain, side view.
PDB entry 8efg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Human and bacterial TatD enzymes exhibit apurinic/apyrimidinic (AP) endonuclease activity.
Dorival J, Eichman BF
OpenAccess logo Nucleic Acids Res (2023)
PMID: 36881763

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-564298 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Deoxyribonuclease TATDN1 Chain: A
Molecule details ›
Chain: A
Length: 295 amino acids
Theoretical weight: 33.4 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6P1N9 (Residues: 2-296; Coverage: 99%)
Gene names: CDA11, TATDN1
Sequence domains: TatD related DNase

Ligands and Environments

6 bound ligands:
Ligand ZN 2 x ZN
Ligand NA 1 x NA
Ligand GOL 4 x GOL
Ligand D5M 2 x D5M
Ligand 3D1 1 x 3D1
Ligand ADE 1 x ADE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 55.88Å b: 76.51Å c: 77.36Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.163 0.189
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Cellular Responses to Widespread DNA Replication Stress.
Nickoloff et al. (2023)
2 other articles

2 mentions without citation

Morphological and Biochemical Diversity of Shallot Landraces Preserved Along the Croatian Coast.
Major et al. (2018)
1 more