3VVV Protein Transport date Jul 28, 2012
title Skich Domain Of Ndp52
authors M.Akutsu, N.V.Muhlinen, F.Randow, D.Komander
compound source
Molecule: Calcium-Binding And Coiled-Coil Domain-Containing 2;
Chain: A
Fragment: Unp Residues 21-141
Synonym: Antigen Nuclear Dot 52 Kda Protein, Nuclear Domain Protein Ndp52, Nuclear Domain 10 Protein 52, Nuclear Dot Pr
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Calcoco2, Ndp52
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.155 R_Free 0.189
crystal
cell
length a length b length c angle alpha angle beta angle gamma
36.610 37.460 90.400 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.35 Å
Primary referenceLC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy., von Muhlinen N, Akutsu M, Ravenhill BJ, Foeglein A, Bloor S, Rutherford TJ, Freund SM, Komander D, Randow F, Mol Cell. 2012 Nov 9;48(3):329-42. doi: 10.1016/j.molcel.2012.08.024. Epub 2012, Sep 27. PMID:23022382
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (49 Kb) [Save to disk]
  • Biological Unit Coordinates (3vvv.pdb1.gz) 89 Kb
  • Biological Unit Coordinates (3vvv.pdb2.gz) 45 Kb
  • CSU: Contacts of Structural Units for 3VVV
  • Structure Factors (1411 Kb)
  • Retrieve 3VVV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VVV from S2C, [Save to disk]
  • Re-refined 3vvv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3VVV 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 3VVV
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3VVV, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vvv] [3vvv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3VVV
  • Community annotation for 3VVV at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science