3NY3 Ligase date Jul 14, 2010
title Structure Of The Ubr-Box Of Ubr2 In Complex With N-Degron
authors E.Matta-Camacho, G.Kozlov, F.Li, K.Gehring
compound source
Molecule: E3 Ubiquitin-Protein Ligase Ubr2
Chain: A
Fragment: Ubr-Box, Unp Residues 98-167
Synonym: N-Recognin-2, Ubiquitin-Protein Ligase E3-Alpha-2, Ubiquitin-Protein Ligase E3-Alpha-II;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ubr2, C6orf133, Kiaa0349
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: N-Degron
Chain: B
Engineered: Yes

Synthetic: Yes
Other_details: Chemically Synthesized Peptide
symmetry Space Group: P 1 21 1
R_factor 0.190 R_Free 0.210
length a length b length c angle alpha angle beta angle gamma
29.123 36.940 29.824 90.00 109.60 90.00
method X-Ray Diffractionresolution 1.60 Å
ligand ZN enzyme Ligase E.C. BRENDA
note 3NY3 is a representative structure

Primary referenceStructural basis of substrate recognition and specificity in the N-end rule pathway., Matta-Camacho E, Kozlov G, Li FF, Gehring K, Nat Struct Mol Biol. 2010 Oct;17(10):1182-7. Epub 2010 Sep 12. PMID:20835242
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (29 Kb) [Save to disk]
  • Biological Unit Coordinates (3ny3.pdb1.gz) 24 Kb
  • LPC: Ligand-Protein Contacts for 3NY3
  • CSU: Contacts of Structural Units for 3NY3
  • Structure Factors (107 Kb)
  • Retrieve 3NY3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NY3 from S2C, [Save to disk]
  • Re-refined 3ny3 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NY3 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 3NY3
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3NY3, from MSDmotif at EBI
  • Fold representative 3ny3 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ny3_A] [3ny3] [3ny3_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 3NY3: [ZnF_UBR1 ] by SMART
  • Other resources with information on 3NY3
  • Community annotation for 3NY3 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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