3N30 Metal Binding Protein date May 19, 2010
title Crystal Structure Of Cubic Zn3-Hub (Human Ubiquitin) Adduct
authors D.Siliqi, R.Caliandro, F.Arnesano, G.Natile, G.Falini, S.Fermani, B.D.Belviso
compound source
Molecule: Ubiquitin
Chain: A, B
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rps27a, Uba80, Ubcep1, Uba52, Ubcep2, Ubb, Ubc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 43 3 2
R_factor 0.234 R_Free 0.318
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.890 104.890 104.890 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand ZN enzyme
Primary referenceCrystallographic analysis of metal-ion binding to human ubiquitin., Arnesano F, Belviso BD, Caliandro R, Falini G, Fermani S, Natile G, Siliqi D, Chemistry. 2011 Feb 1;17(5):1569-78. doi: 10.1002/chem.201001617. Epub, 2010 Dec 10. PMID:21268159
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (3n30.pdb1.gz) 13 Kb
  • Biological Unit Coordinates (3n30.pdb2.gz) 13 Kb
  • LPC: Ligand-Protein Contacts for 3N30
  • CSU: Contacts of Structural Units for 3N30
  • Structure Factors (223 Kb)
  • Retrieve 3N30 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3N30 from S2C, [Save to disk]
  • Re-refined 3n30 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3N30 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 3N30
  • 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 3N30, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3n30] [3n30_A] [3n30_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3N30: [UBQ ] by SMART
    • Other resources with information on 3N30
  • Community annotation for 3N30 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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