4JHP Lipid Binding Protein date Mar 05, 2013
title The Crystal Structure Of The Rpgr Rcc1-Like Domain In Comple Pde6d
authors D.Waetzlich, I.Vetter, A.Wittinghofer, S.Ismail
compound source
Molecule: Retinal Rod Rhodopsin-Sensitive Cgmp 3',5'-Cyclic Phosphodiesterase Subunit Delta;
Chain: B
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: X-Linked Retinitis Pigmentosa Gtpase Regulator
Chain: C
Fragment: Rpgr (8-368) The Rcc1-Like Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rpgr, Rp3, Xlrp3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: C 1 2 1
R_factor 0.200 R_Free 0.221
length a length b length c angle alpha angle beta angle gamma
133.830 58.780 92.110 90.00 123.32 90.00
method X-Ray Diffractionresolution 1.90 Å

Primary referenceThe interplay between RPGR, PDEdelta and Arl2/3 regulate the ciliary targeting of farnesylated cargo., Watzlich D, Vetter I, Gotthardt K, Miertzschke M, Chen YX, Wittinghofer A, Ismail S, EMBO Rep. 2013 Apr 5. doi: 10.1038/embor.2013.37. PMID:23559067
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (92 Kb) [Save to disk]
  • Biological Unit Coordinates (4jhp.pdb1.gz) 87 Kb
  • CSU: Contacts of Structural Units for 4JHP
  • Structure Factors (366 Kb)
  • Retrieve 4JHP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4JHP from S2C, [Save to disk]
  • Re-refined 4jhp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4JHP in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4JHP
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • 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
  • 3D motif for 4JHP, from MSDmotif at EBI
  • Fold representative 4jhp from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4jhp] [4jhp_B] [4jhp_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4JHP with the sequences similar proteins can be viewed for 4JHP's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4JHP
  • Community annotation for 4JHP at PDBWiki (http://pdbwiki.org)

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