› 5oca

X-ray diffraction
2.3Å resolution

PCSK9:Fab Complex with Dextran Sulfate

Released:
DOI: 10.2210/pdb5oca/pdb
PDB entry 5oca coloured by chain, front view.
PDB entry 5oca coloured by chain, side view.
PDB entry 5oca coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Heparan sulfate proteoglycans present PCSK9 to the LDL receptor.
Gustafsen C, Olsen D, Vilstrup J, Lund S, Reinhardt A, Wellner N, Larsen T, Andersen CBF, Weyer K, Li JP, Seeberger PH, Thirup S, Madsen P, Glerup S
Nat Commun 8 503 (2017)
PMID: 28894089

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212626 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (5 distinct):
Proprotein convertase subtilisin/kexin type 9 Chain: A
Molecule details ›
Chain: A
Length: 126 amino acids
Theoretical weight: 14.11 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8NBP7 (Residues: 31-152; Coverage: 18%)
Gene names: NARC1, PCSK9, PSEC0052
Sequence domains: Peptidase inhibitor I9
Structure domains: Peptidase S8 propeptide/proteinase inhibitor I9
Proprotein convertase subtilisin/kexin type 9 Chain: B
Molecule details ›
Chain: B
Length: 540 amino acids
Theoretical weight: 57.33 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8NBP7 (Residues: 153-692; Coverage: 82%)
Gene names: NARC1, PCSK9, PSEC0052
Sequence domains:
Structure domains:
Fab from LDLR competitive antibody: Heavy chain Chain: H
Molecule details ›
Chain: H
Length: 238 amino acids
Theoretical weight: 25.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Fab from LDLR competitive antibody: Light chain Chain: L
Molecule details ›
Chain: L
Length: 217 amino acids
Theoretical weight: 22.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

Carbohydrate polymer : NEW Components: TWD, TWA
Carbohydrate polymer
1 bound ligand:
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: C2
Unit cell:
a: 264.721Å b: 137.352Å c: 69.885Å
α: 90° β: 102.84° γ: 90°
R-values:
R R work R free
0.169 0.167 0.195
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

Quick links

Citations

9 review citations

Mechanisms and regulation of cholesterol homeostasis.
Luo et al. (2020)
8 more

4 mentions without citation

Heparan sulfate proteoglycans present PCSK9 to the LDL receptor.
Gustafsen et al. (2017)
3 more