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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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


Macromolecules
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Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GER (Subject of Investigation/LOI)
Query on GER

Download Ideal Coordinates CCD File 
E [auth D], F [auth E]GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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