2PMW | pdb_00002pmw

The Crystal Structure of Proprotein convertase subtilisin kexin type 9 (PCSK9)

• PDB DOI: https://doi.org/10.2210/pdb2PMW/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 2007-04-23 Released: 2007-05-08 
• Deposition Author(s): Piper, D.E., Romanow, W.G., Thibault, S.T., Walker, N.P.C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.196 (DCC) 

Literature

The Crystal Structure of PCSK9: A Regulator of Plasma LDL-Cholesterol.

Piper, D.E., Jackson, S., Liu, Q., Romanow, W.G., Shetterly, S., Thibault, S.T., Shan, B., Walker, N.P.

(2007) Structure 15: 545-552

• PubMed: 17502100 
• DOI: https://doi.org/10.1016/j.str.2007.04.004
• Primary Citation Related Structures: 
  2PMW


• PubMed Abstract: 
  

  Proprotein convertase subtilisin kexin type 9 (PCSK9) has been shown to be involved in the regulation of extracellular levels of the low-density lipoprotien receptor (LDLR). Although PCSK9 is a subtilase, it has not been shown to degrade the LDLR, and its LDLR-lowering mechanism remains uncertain. Here we report the crystal structure of human PCSK9 at 2.3 A resolution. PCSK9 has subtilisin-like pro- and catalytic domains, and the stable interaction between these domains prevents access to PCSK9's catalytic site. The C-terminal domain of PCSK9 has a novel protein fold and may mediate protein-protein interactions. The structure of PCSK9 provides insight into its biochemical characteristics and biological function.

---

Organizational Affiliation: 
• Department of Molecular Structure, Amgen Inc., 1120 Veterans Boulevard, South San Francisco, California 94080, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 71.66 kDa 
• Atom Count: 4,583 
• Modeled Residue Count: 581 
• Deposited Residue Count: 666 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	A	126	Homo sapiens	Mutation(s): 0  Gene Names: PCSK9, NARC1 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens) Explore Q8NBP7  Go to UniProtKB:  Q8NBP7
PHAROS:  Q8NBP7 GTEx:  ENSG00000169174

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	B	540	Homo sapiens	Mutation(s): 0  EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NBP7 (Homo sapiens) Explore Q8NBP7  Go to UniProtKB:  Q8NBP7
PHAROS:  Q8NBP7 GTEx:  ENSG00000169174

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.232 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.196 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.106	α = 90
b = 70.709	β = 90
c = 150.693	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SOLVE	phasing
CNS	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Piper, D.E., Romanow, W.G., Thibault, S.T., Walker, N.P.C.

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary