8WFR | pdb_00008wfr

The Crystal Structure of PCSK9 from Biortus.

• PDB DOI: https://doi.org/10.2210/pdb8WFR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-09-20 Released: 2023-11-22 
• Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Meng, Q., Lu, Y.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 

Starting Model: experimental

Literature

The Crystal Structure of PCSK9 from Biortus.

Wang, F., Cheng, W., Lv, Z., Meng, Q., Lu, Y.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 71.81 kDa 
• Atom Count: 4,752 
• Modeled Residue Count: 571 
• Deposited Residue Count: 664 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	A	124	Homo sapiens	Mutation(s): 0  Gene Names: PCSK9 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  Gene Names: PCSK9 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE (Subject of Investigation/LOI)	C [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)	E [auth A], G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	D [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.081	α = 90
b = 70.813	β = 90
c = 149.867	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Wang, F., Cheng, W., Lv, Z., Meng, Q., Lu, Y.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Structure summary