› 4ydg

X-ray diffraction
3.25Å resolution

Crystal structure of compound 10 in complex with HTLV-1 Protease

Released:
DOI: 10.2210/pdb4ydg/pdb
PDB entry 4ydg coloured by chain, front view.
PDB entry 4ydg coloured by chain, side view.
PDB entry 4ydg coloured by chain, top view.
Source organism: Human T-cell lymphotrophic virus type 1 (strain ATK)
Primary publication:
Privileged Structures Meet Human T-Cell Leukemia Virus-1 (HTLV-1): C2-Symmetric 3,4-Disubstituted Pyrrolidines as Nonpeptidic HTLV-1 Protease Inhibitors.
Kuhnert M, Blum A, Steuber H, Diederich WE
J Med Chem 58 4845-50 (2015)
PMID: 26000468

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Endonucleolytic cleavage to 5'-phosphomonoester.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136832 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 116 amino acids
Theoretical weight: 12.57 KDa
Source organism: Human T-cell lymphotrophic virus type 1 (strain ATK)
Expression system: Escherichia coli
UniProt:
  • Canonical: P03362 (Residues: 450-565; Coverage: 8%)
Gene name: gag-pro-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

2 bound ligands:
Ligand SO4 2 x SO4
Ligand G3G 1 x G3G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P6322
Unit cell:
a: 77.61Å b: 77.61Å c: 160.23Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.281 0.279 0.317
Expression system: Escherichia coli

Quick links

Citations

11 citation in other articles

Alkenyl Arenes as Dipolarophiles in Catalytic Asymmetric 1,3-Dipolar Cycloaddition Reactions of Azomethine Ylides.
Pascual-Escudero et al. (2016)
10 more

3 mentions without citation

Dimer Interface Organization is a Main Determinant of Intermonomeric Interactions and Correlates with Evolutionary Relationships of Retroviral and Retroviral-Like Ddi1 and Ddi2 Proteases.
Mótyán et al. (2020)
2 more