4W9H pVHL:EloB:EloC in complex with (2S,4R)-1-((S)-2-acetamido-3,3-dimethylbutanoyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (ligand 7) date
authors Gadd, M.S., Soares, P., Galdeano, C., Molle, I.van., Ciulli, A.
compound source
symmetry
R_factor
R_Free 0.2533
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.10
ligand 3JF, CAS enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


H, K, E, B


Primary referenceStructure-Guided Design and Optimization of Small Molecules Targeting the Protein-Protein Interaction between the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase and the Hypoxia Inducible Factor (HIF) Alpha Subunit with In Vitro Nanomolar Affinities., Galdeano C, Gadd MS, Soares P, Scaffidi S, Van Molle I, Birced I, Hewitt S, Dias DM, Ciulli A, J Med Chem. 2014 Aug 28. PMID:25166285
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (453 Kb) [Save to disk]
  • Biological Unit Coordinates (4w9h.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (4w9h.pdb2.gz) 113 Kb
  • Biological Unit Coordinates (4w9h.pdb3.gz) 114 Kb
  • Biological Unit Coordinates (4w9h.pdb4.gz) 115 Kb
  • LPC: Ligand-Protein Contacts for 4W9H
  • CSU: Contacts of Structural Units for 4W9H
  • Structure Factors (1731 Kb)
  • Retrieve 4W9H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4W9H from S2C, [Save to disk]
  • Re-refined 4w9h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 4W9H 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 4W9H
  • 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 4W9H, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4w9h_J] [4w9h_K] [4w9h_I] [4w9h_H] [4w9h_G] [4w9h] [4w9h_F] [4w9h_C] [4w9h_B] [4w9h_A] [4w9h_D] [4w9h_L] [4w9h_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4W9H: [Skp1] [UBQ ] by SMART
    • Other resources with information on 4W9H
  • Community annotation for 4W9H at PDBWiki (http://pdbwiki.org)

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