› 1cpi

X-ray diffraction
2.05Å resolution

REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES. DESIGN OF HYDROLYTICALLY STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE

Released:
DOI: 10.2210/pdb1cpi/pdb
PDB entry 1cpi coloured by chain, front view.
PDB entry 1cpi coloured by chain, side view.
PDB entry 1cpi coloured by chain, top view.
Source organism: HIV-1 M:B_ARV2/SF2
Primary publication:
REGIOSELECTIVE STRUCTURAL AND FUNCTIONAL MIMICRY OF PEPTIDES - DESIGN OF HYDROLYTICALLY-STABLE CYCLIC PEPTIDOMIMETIC INHIBITORS OF HIV-1 PROTEASE.
Abbenante G, March DR, Bergman DA, Hunt PA, Garnham B, Dancer RJ, Martin JL, Fairlie DP
J. Am. Chem. Soc. 117 10220-10226 (1995)

Function and Biology Details

Reactions catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136883 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Protease Chains: A, B
Molecule details ›
Chains: A, B
Length: 99 amino acids
Theoretical weight: 10.76 KDa
Source organism: HIV-1 M:B_ARV2/SF2
Expression system: Not provided
UniProt:
  • Canonical: P03369 (Residues: 491-589; Coverage: 7%)
Gene name: gag-pol
Sequence domains: Retroviral aspartyl protease
Structure domains: Acid Proteases
CYCLIC PEPTIDE INHIBITOR Chain: C
Molecule details ›
Chain: C
Length: 6 amino acids
Theoretical weight: 768 Da
Source organism: HIV-1 M:B_ARV2/SF2
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 3 x SO4
1 modified residue:
Ligand ABA 4 x ABA

Experiments and Validation Details

Entry percentile scores
Spacegroup: P212121
Unit cell:
a: 51.3Å b: 58.8Å c: 62.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.163 0.163 0.237
Expression system: Not provided

Quick links

Citations

3 mentions without citation

X-ray crystal structure of the cytochrome P450 2B4 active site mutant F297A in complex with clopidogrel: insights into compensatory rearrangements of the binding pocket.
Shah et al. (2013)
2 more