5E8F

Structure of Fully modified geranylgeranylated PDE6C Peptide in complex with PDE6D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The N- and C-terminal ends of RPGR can bind to PDE6 delta.

Fansa, E.K.O'Reilly, N.J.Ismail, S.Wittinghofer, A.

(2015) EMBO Rep 16: 1583-1585

  • DOI: https://doi.org/10.15252/embr.201541404
  • Primary Citation of Related Structures:  
    5E8F

  • PubMed Abstract: 

    This study shows that the prenylated C‐terminus of RPGR can bind to PDE6δ with high affinity, suggesting two distinct binding sites of the RPGR/PDE6δ complex. The serine residue at the −3 position relative to the prenylated cysteine seems to play a key role in defining the selectivity of PDE6δ towards ciliary prenylated cargo. [Image: see text]


  • Organizational Affiliation

    Max Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit deltaA,
B [auth C]
149Homo sapiensMutation(s): 0 
Gene Names: PDE6DPDED
EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for O43924 (Homo sapiens)
Explore O43924 
Go to UniProtKB:  O43924
PHAROS:  O43924
GTEx:  ENSG00000156973 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43924
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'C [auth D],
D [auth E]
5Homo sapiensMutation(s): 0 
Gene Names: PDE6CPDEA2
EC: 3.1.4.35
UniProt & NIH Common Fund Data Resources
Find proteins for P51160 (Homo sapiens)
Explore P51160 
Go to UniProtKB:  P51160
PHAROS:  P51160
GTEx:  ENSG00000095464 
Entity Groups  
UniProt GroupP51160
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CMT
Query on CMT
C [auth D],
D [auth E]
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.71α = 90
b = 81.43β = 90
c = 118.53γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description