2KNV Protein Binding date Sep 04, 2009
title Nmr Dimer Structure Of The Uba Domain Of P62 (Sqstm1)
authors J.E.Long, M.S.Searle
compound source
Molecule: Sequestosome-1
Chain: A, B
Fragment: Uba Domain, Unp Residues 387-436
Synonym: Phosphotyrosine-Independent Ligand For The Lck Sh2 Domain Of 62 Kda, Ubiquitin-Binding Protein P62, Ebi3- Associated Protein Of 60 Kda, P60, Ebiap;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sqstm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21
Expression_system_variant: (De3)
Expression_system_vector_type: Vector
Expression_system_vector: Pgex-4t-1
methodSolution NMR
Primary referenceDimerisation of the UBA Domain of p62 Inhibits Ubiquitin Binding and Regulates NF-kappaB Signalling., Long J, Garner TP, Pandya MJ, Craven CJ, Chen P, Shaw B, Williamson MP, Layfield R, Searle MS, J Mol Biol. 2009 Nov 17. PMID:19931284
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (268 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 2KNV
  • Original NMR restraints for 2KNV from PDB
  • Retrieve 2KNV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2KNV from S2C, [Save to disk]
  • View 2KNV 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 2KNV
  • 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 2KNV, from MSDmotif at EBI
  • Fold representative 2knv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2knv] [2knv_B] [2knv_A]
  • SWISS-PROT database: [Q13501]
  • Domain organization of [SQSTM_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 2KNV with the sequences similar proteins can be viewed for 2KNV's classification [SQSTM_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 [SQSTM_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 2KNV
  • Community annotation for 2KNV 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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