4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action date
authors Scott, D.C., Schulman, B.A.
compound source
symmetry
R_factor
R_Free 0.2843
crystal
cell
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 3.11
ligand AME, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


B, D


I, G


K, H


Primary referenceStructure of a RING E3 Trapped in Action Reveals Ligation Mechanism for the Ubiquitin-like Protein NEDD8., Scott DC, Sviderskiy VO, Monda JK, Lydeard JR, Cho SE, Harper JW, Schulman BA, Cell. 2014 Jun 19;157(7):1671-84. doi: 10.1016/j.cell.2014.04.037. PMID:24949976
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (586 Kb) [Save to disk]
  • Biological Unit Coordinates (4p5o.pdb1.gz) 289 Kb
  • Biological Unit Coordinates (4p5o.pdb2.gz) 287 Kb
  • LPC: Ligand-Protein Contacts for 4P5O
  • CSU: Contacts of Structural Units for 4P5O
  • Structure Factors (573 Kb)
  • Retrieve 4P5O in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4P5O from S2C, [Save to disk]
  • Re-refined 4p5o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4P5O 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 4P5O
  • 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 4P5O, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4p5o_G] [4p5o_K] [4p5o_B] [4p5o_F] [4p5o_D] [4p5o_E] [4p5o_A] [4p5o_I] [4p5o_H] [4p5o] [4p5o_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4P5O: [CULLIN] [Cullin_Nedd8] [RING] [UBCc] [UBQ ] by SMART
  • Other resources with information on 4P5O
  • Community annotation for 4P5O at PDBWiki (http://pdbwiki.org)

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