3B7Y Ligase date Oct 31, 2007
title Crystal Structure Of The C2 Domain Of The E3 Ubiquitin-Prote Nedd4
authors J.R.Walker, M.Ruzanov, C.Butler-Cole, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics C (Sgc)
compound source
Molecule: E3 Ubiquitin-Protein Ligase Nedd4
Chain: A, B
Fragment: C2 Domain: Residues 101-252
Ec: 6.3.2.-
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nedd4, Kiaa0093
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P28a-Lic-Tev
symmetry Space Group: P 1
R_factor 0.169 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.778 47.997 50.786 108.89 111.11 100.86
method X-Ray Diffractionresolution 1.80 Å
ligand CA enzyme Ligase E.C.6.3.2 BRENDA
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (107 Kb) [Save to disk]
  • Biological Unit Coordinates (3b7y.pdb1.gz) 50 Kb
  • Biological Unit Coordinates (3b7y.pdb2.gz) 51 Kb
  • LPC: Ligand-Protein Contacts for 3B7Y
  • CSU: Contacts of Structural Units for 3B7Y
  • Likely Quarternary Molecular Structure file(s) for 3B7Y
  • Structure Factors (385 Kb)
  • Retrieve 3B7Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3B7Y from S2C, [Save to disk]
  • Re-refined 3b7y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3B7Y 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 3B7Y
  • 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 3B7Y, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3b7y] [3b7y_A] [3b7y_B]
  • SWISS-PROT database: [P46934]
  • Belongs to the nedd4-family interacting protein-2 (nedd4) family according to TCDB.
  • Domain organization of [NEDD4_HUMAN] by SWISSPFAM
  • Domain found in 3B7Y: [C2 ] by SMART
    • Other resources with information on 3B7Y
  • Community annotation for 3B7Y 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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