8VDV | pdb_00008vdv

pcsk9 in complex with inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

PCSK9 in complex with inhibitor

Xu, M., Xu, M.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 992Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proprotein convertase subtilisin/kexin type 9529Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NBP7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEHC [auth L]11synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
BIF
Query on BIF		C [auth L]L-PEPTIDE LINKINGC15 H15 N O2PHE
EME
Query on EME		C [auth L]L-PEPTIDE LINKINGC6 H11 N O4GLU
MAA
Query on MAA		C [auth L]L-PEPTIDE LINKINGC4 H9 N O2ALA
PHA
Query on PHA		C [auth L]L-PEPTIDE LINKINGC9 H11 N OPHE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.086α = 90
b = 70.846β = 90
c = 149.007γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release