3NIK	Metal Binding Protein	date	Jun 16, 2010
title	The Structure Of Ubr Box (Reaa)
authors	W.S.Choi, B.C.Jeong, M.R.Lee, H.K.Song
compound		source
Molecule: E3 Ubiquitin-Protein Ligase Ubr1 Chain: A, B, D, F Fragment: Ubr-Type Domain, Residues 115-194 Synonym: N-Recognin-1, N-End-Recognizing Protein Engineered: Yes Other_details: Ubr Box		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Expression_system: Escherichia Coli Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Ril Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet
Molecule: Peptide Reaa Chain: X Engineered: Yes		Synthetic: Yes Other_details: Chemical Synthesis
symmetry	Space Group: P 32	R_factor 0.191 R_Free 0.243
crystal cell	length a length b length c angle alpha angle beta angle gamma 44.534 44.534 139.636 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	1.85 Å
ligand	ZN	enzyme
Gene Ontology	Chain Function Process Component F, A, D, B
Primary reference	Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases., Choi WS, Jeong BC, Joo YJ, Lee MR, Kim J, Eck MJ, Song HK, Nat Struct Mol Biol. 2010 Sep 12. PMID:20835240

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (66 Kb) [Save to disk] Biological Unit Coordinates (3nik.pdb1.gz) 17 Kb Biological Unit Coordinates (3nik.pdb2.gz) 16 Kb Biological Unit Coordinates (3nik.pdb3.gz) 17 Kb Biological Unit Coordinates (3nik.pdb4.gz) 16 Kb LPC: Ligand-Protein Contacts for 3NIK CSU: Contacts of Structural Units for 3NIK Structure Factors (393 Kb) Retrieve 3NIK in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3NIK from S2C, [Save to disk] Re-refined 3nik structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3NIK 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 3NIK

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 3NIK, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3nik_D] [3nik_X] [3nik_F] [3nik_B] [3nik] [3nik_A] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 3NIK: [ZnF_UBR1 ] by SMART

Other resources with information on 3NIK

Community annotation for 3NIK at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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