3M0C | pdb_00003m0c

The X-ray Crystal Structure of PCSK9 in Complex with the LDL receptor

• PDB DOI: https://doi.org/10.2210/pdb3M0C/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2010-03-02 Released: 2011-03-16 
• Deposition Author(s): Spraggon, G., Hampton, E.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 7.01 Å
• R-Value Free: 
  0.362 (Depositor), 0.353 (DCC) 
• R-Value Work: 
  0.341 (Depositor), 0.339 (DCC) 
• R-Value Observed: 
  0.342 (Depositor) 

Starting Models: experimental

Literature

The X-ray Crystal Structure of PCSK9 in Complex with the LDL receptor

Li, J., Gavigan, J.A., Zheng, G., Huang, W., Yowe, D., Geisse, S., Harris, J.L., Lesley, S.A., Spraggon, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 160.15 kDa 
• Atom Count: 7,705 
• Modeled Residue Count: 1,008 
• Deposited Residue Count: 1,461 
• Unique protein chains: 3

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: NARC1, PCSK9, 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	546	Homo sapiens	Mutation(s): 1  Gene Names: NARC1, PCSK9, 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
Low-density lipoprotein receptor	C	791	Homo sapiens	Mutation(s): 0  Gene Names: LDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P01130 (Homo sapiens) Explore P01130  Go to UniProtKB:  P01130
PHAROS:  P01130 GTEx:  ENSG00000130164

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 7.01 Å
• R-Value Free:  0.362 (Depositor), 0.353 (DCC) 
• R-Value Work:  0.341 (Depositor), 0.339 (DCC) 
• R-Value Observed: 0.342 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 322.906	α = 90
b = 322.906	β = 90
c = 76.733	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Spraggon, G., Hampton, E.N.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-27
  Changes: Structure summary