3DPL Ligase date Jul 08, 2008
title Structural Insights Into Nedd8 Activation Of Cullin-Ring Lig Conformational Control Of Conjugation.
authors D.M.Duda, B.A.Schulman
compound source
Molecule: Cullin-5
Chain: C
Fragment: Residues 401-780
Synonym: Cul-5, Vasopressin-Activated Calcium-Mobilizing Re Vacm-1;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Cul5, Vacm1
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)Gold
Expression_system_plasmid: Pgex4t1

Molecule: Ring-Box Protein 1
Chain: R
Synonym: Rbx1, Regulator Of Cullin-1, Ring Finger Protein 7 Zyp;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Gene: Rbx1, Rnf75, Roc1
Expression_system: Escherichia Coli
Expression_system_strain: Bl21(De3)Gold
Expression_system_plasmid: Prsf-Duet
symmetry Space Group: P 21 21 21
R_factor 0.244 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
62.965 65.510 141.116 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.60 Å
ligand ZN enzyme
note 3DPL is a representative structure
Gene
Ontology
ChainFunctionProcessComponent
C


R


Primary referenceStructural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation., Duda DM, Borg LA, Scott DC, Hunt HW, Hammel M, Schulman BA, Cell. 2008 Sep 19;134(6):995-1006. PMID:18805092
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (3dpl.pdb1.gz) 79 Kb
  • LPC: Ligand-Protein Contacts for 3DPL
  • CSU: Contacts of Structural Units for 3DPL
  • Likely Quarternary Molecular Structure file(s) for 3DPL
  • Structure Factors (138 Kb)
  • Retrieve 3DPL in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DPL from S2C, [Save to disk]
  • Re-refined 3dpl structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DPL 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 3DPL
  • 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 3DPL, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dpl] [3dpl_C] [3dpl_R]
  • SWISS-PROT database: [Q93034] [P62877]
  • Domain organization of [CUL5_HUMAN] [RBX1_HUMAN] by SWISSPFAM
  • Domains found in 3DPL: [CULLIN] [Cullin_Nedd8] [RING ] by SMART
  • Other resources with information on 3DPL
  • Community annotation for 3DPL at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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