8T8R | pdb_00008t8r

Sortilin-PGRN peptide complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free: 
    0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.258 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 
    0.259 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history. 


Literature

Structural studies of Sortilin-PGRN peptide complex

Srivastava, D.B., Cherf, G.M., Low, L.Y., Kannan, G.

To be published.

Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sortilin678Homo sapiensMutation(s): 0 
Gene Names: SORT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99523 (Homo sapiens)
Explore Q99523 
Go to UniProtKB:  Q99523
PHAROS:  Q99523
GTEx:  ENSG00000134243 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99523
Glycosylation
Glycosylation Sites: 4
Go to GlyGen: Q99523-1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Paragranulin peptide16Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P28799 (Homo sapiens)
Explore P28799 
Go to UniProtKB:  P28799
PHAROS:  P28799
GTEx:  ENSG00000030582 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28799
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.87 Å
  • R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.258 (Depositor), 0.250 (DCC) 
  • R-Value Observed: 0.259 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.945α = 90
b = 78.618β = 126.8
c = 111.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary