5E8F Hydrolase date Oct 14, 2015
title Structure Of Fully Modified Geranylgeranylated Pde6c Peptide Complex With Pde6d
authors E.K.Fansa, N.J.O'Reilly, S.A.Ismail, A.Wittinghofer
compound source
Molecule: Retinal Rod Rhodopsin-Sensitive Cgmp 3',5'-Cyclic Phosphodiesterase Subunit Delta;
Chain: A, C
Fragment: Unp Residues 2-150
Synonym: Gmp-Pde Delta,Protein P17
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde6d, Pded
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Cone Cgmp-Specific 3',5'-Cyclic Phosphodiesterase Alpha';
Chain: D, E
Fragment: Unp Residues 851-855
Synonym: Cgmp Phosphodiesterase 6c
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pde6c, Pdea2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 2 2 21
R_factor 0.198 R_Free 0.256
length a length b length c angle alpha angle beta angle gamma
77.710 81.430 118.530 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CMT, GER enzyme Hydrolase E.C. BRENDA
A, C
  • GTPase inhibitor activity

  • Primary referenceThe N- and C-terminal ends of RPGR can bind to PDE6delta., Fansa EK, O'Reilly NJ, Ismail S, Wittinghofer A, EMBO Rep. 2015 Dec;16(12):1583-5. doi: 10.15252/embr.201541404. Epub 2015 Nov 9. PMID:26553937
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (59 Kb) [Save to disk]
  • Biological Unit Coordinates (5e8f.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (5e8f.pdb2.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 5E8F
  • CSU: Contacts of Structural Units for 5E8F
  • Structure Factors (475 Kb)
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  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5e8f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5e8f_C] [5e8f_D] [5e8f] [5e8f_A] [5e8f_E]
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