1IYF Ligase date Aug 13, 2002
title Solution Structure Of Ubiquitin-Like Domain Of Human Parkin
authors E.Sakata, Y.Yamaguchi, E.Kurimoto, J.Kikuchi, S.Yokoyama, H.Kawahara, H.Yokosawa, N.Hattori, Y.Mizuno, K.Tanaka, K.Kato, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Parkin
Chain: A
Fragment: Ubiquitin-Like Domain
Ec: 6.3.2.19
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex6p3
methodSolution NMR
ligand
enzyme Ligase E.C.6.3.2.19 BRENDA
related structures by homologous chain: 1MG8
Primary referenceParkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain., Sakata E, Yamaguchi Y, Kurimoto E, Kikuchi J, Yokoyama S, Yamada S, Kawahara H, Yokosawa H, Hattori N, Mizuno Y, Tanaka K, Kato K, EMBO Rep 2003 Mar;4(3):301-6. PMID:12634850
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (211 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 1IYF
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1IYF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IYF from S2C, [Save to disk]
    • View 1IYF 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.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1IYF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1IYF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1iyfa_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1iyf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1iyf_A]
  • SWISS-PROT database: [O60260]
  • Domain organization of [PRKN2_HUMAN] by SWISSPFAM
  • Domain found in 1IYF: [UBQ ] by SMART
  • Alignments of the sequence of 1IYF with the sequences similar proteins can be viewed for 1IYF's classification [PRKN2_HUMAN] 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 [PRKN2_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1IYF
  • Community annotation for 1IYF at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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