8FVP

PCSK9 in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb8FVP/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-01-19 Released: 2024-10-16 
• Deposition Author(s): Xu, M., Chopra, R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

pcsk9 in complex with cyclic peptide

Xu, M., Chopra, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 75.47 kDa 
• Atom Count: 4,424 
• Modelled Residue Count: 578 
• Deposited Residue Count: 701 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proprotein convertase subtilisin/kexin type 9	A	152	Homo sapiens	Mutation(s): 0  Gene Names: PCSK9, NARC1, PSEC0052 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): 2  Gene Names: PCSK9, NARC1, PSEC0052 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PPI-YD5-NLE-7T2-SER-7T2-DPP-GLY-NH2 inhibitor	C [auth L]	9	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
7T2	C [auth L]	L-PEPTIDE LINKING	C10 H12 Cl N O2		PHE
DPP	C [auth L]	L-PEPTIDE LINKING	C3 H8 N2 O2		ALA
NLE	C [auth L]	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002525	C [auth L]	PPI-YD5-NLE-7T2-SER-7T2-DPP-GLY-NH2 inhibitor	Cyclic peptide / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.033	α = 90
b = 70.407	β = 90
c = 150.112	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
HKL-2000	data reduction
FFT	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Xu, M., Chopra, R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release