4J5D Human Cyclophilin D Complexed with an Inhibitor date 2013-02-08
authors Gelin, M., Colliandre, L., Bessin, Y., Guichou, J.F.
compound source
symmetry
R_factor
R_Free 0.1625
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 1.32
ligand 728 enzyme
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 (4j5d.pdb1.gz) 67 Kb
  • LPC: Ligand-Protein Contacts for 4J5D
  • CSU: Contacts of Structural Units for 4J5D
  • Structure Factors (390 Kb)
  • Retrieve 4J5D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4J5D from S2C, [Save to disk]
  • Re-refined 4j5d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4J5D 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 4J5D
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 4J5D, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4j5d] [4j5d_X]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4J5D
  • Community annotation for 4J5D at PDBWiki (http://pdbwiki.org)

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