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
  • Alignments of the sequence of 3NY3 with the sequences similar proteins can be viewed for 3NY3's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • 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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