3RDA Isomerase Isomerase Inhibitor date Apr 01, 2011
title Human Cyclophilin D Complexed With A Fragment
authors L.Colliandre, H.Ahmed-Belkacem, Y.Bessin, J.M.Pawlotsky, J.F.Gui
compound source
Molecule: Peptidyl-Prolyl Cis-Trans Isomerase F, Mitochondr
Chain: X
Fragment: Unp Residues 43-207
Synonym: Ppiase F, Cyclophilin F, Rotamase F
Ec: 5.2.1.8
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ppif, Cyp3
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 41 21 2
R_factor 0.115 R_Free 0.138
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.222 57.222 87.009 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.07 Å
ligand MIO enzyme Isomerase E.C.5.2.1.8 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
X


Primary referenceFragment-based discovery of a new family of non-peptidic small-molecule cyclophilin inhibitors with potent antiviral activities., Ahmed-Belkacem A, Colliandre L, Ahnou N, Nevers Q, Gelin M, Bessin Y, Brillet R, Cala O, Douguet D, Bourguet W, Krimm I, Pawlotsky JM, Guichou JF, Nat Commun. 2016 Sep 22;7:12777. doi: 10.1038/ncomms12777. PMID:27652979
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (3rda.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 3RDA
  • CSU: Contacts of Structural Units for 3RDA
  • Structure Factors (896 Kb)
  • Retrieve 3RDA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RDA from S2C, [Save to disk]
  • Re-refined 3rda structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RDA 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 3RDA
  • 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
  • 3D motif for 3RDA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rda] [3rda_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3RDA
  • Community annotation for 3RDA at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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