› 5vlk

X-ray diffraction
2.2Å resolution

Short PCSK9 delta-P' complex with shrunken peptide bearing homo-Arginine

Released:
DOI: 10.2210/pdb5vlk/pdb
PDB entry 5vlk coloured by chain, front view.
PDB entry 5vlk coloured by chain, side view.
PDB entry 5vlk coloured by chain, top view.
Source organisms:
Primary publication:
Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists.
Zhang Y, Ultsch M, Skelton NJ, Burdick DJ, Beresini MH, Li W, Kong-Beltran M, Peterson A, Quinn J, Chiu C, Wu Y, Shia S, Moran P, Di Lello P, Eigenbrot C, Kirchhofer D
Nat Struct Mol Biol 24 848-856 (2017)
PMID: 28825733

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-166223 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Proprotein convertase subtilisin/kexin type 9 Chain: A
Molecule details ›
Chain: A
Length: 460 amino acids
Theoretical weight: 49.78 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q8NBP7 (Residues: 1-452; Coverage: 64%)
Gene names: NARC1, PCSK9, PSEC0052
Sequence domains:
ACE-THR-VAL-PHE-THR-SER-TRP-GLU-GLU-TYR-LEU-ASP-TRP-VAL-NH2 peptide Chain: Y
Molecule details ›
Chain: Y
Length: 15 amino acids
Theoretical weight: 1.7 KDa
Source organism: synthetic construct
Expression system: Not provided
ACE-TRP-ASN-LEU-VAL-HRG-ILE-GLY-LEU-LEU peptide Chain: Z
Molecule details ›
Chain: Z
Length: 11 amino acids
Theoretical weight: 1.28 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 1 x CA
1 modified residue:
Ligand HRG 1 x HRG

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P3221
Unit cell:
a: 70.387Å b: 70.387Å c: 156.983Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.197 0.195 0.237
Expression systems:
  • Spodoptera frugiperda
  • Not provided

Quick links

Citations

6 review citations

PCSK9: From Basic Science Discoveries to Clinical Trials.
Shapiro et al. (2018)
5 more