› 4iqv

X-ray diffraction
2.9Å resolution

Tdt core in complex with inhibitor 6-[4-(3-fluorobenzoyl)-1H-pyrrol-2-yl]-2-hydroxy-4-oxohexa-2,5-dienoic acid and ssDNA

Released:
DOI: 10.2210/pdb4iqv/pdb
PDB entry 4iqv coloured by chain, front view.
PDB entry 4iqv coloured by chain, side view.
PDB entry 4iqv coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
New nucleotide-competitive non-nucleoside inhibitors of terminal deoxynucleotidyl transferase: discovery, characterization, and crystal structure in complex with the target.
Costi R, Crucitti GC, Pescatori L, Messore A, Scipione L, Tortorella S, Amoroso A, Crespan E, Campiglia P, Maresca B, Porta A, Granata I, Novellino E, Gouge J, Delarue M, Maga G, Di Santo R
J Med Chem 56 7431-41 (2013)
PMID: 23968551

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117652 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA nucleotidylexotransferase Chain: A
Molecule details ›
Chain: A
Length: 400 amino acids
Theoretical weight: 45.66 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P09838 (Residues: 132-510; Coverage: 74%)
Gene names: Dntt, Tdt
Sequence domains:
Structure domains:
5'-D(*GP*CP*CP*G)-3' Chain: C
Molecule details ›
Chain: C
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NA 1 x NA
Ligand 1FO 1 x 1FO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P212121
Unit cell:
a: 46.86Å b: 84.54Å c: 122.95Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.179 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 citation in other articles

Aberrant RAG-mediated recombination contributes to multiple structural rearrangements in lymphoid blast crisis of chronic myeloid leukemia.
Thomson et al. (2020)
8 more