3KB5 Membrane Protein date Oct 20, 2009
title Pry-Spry Domain Of Human Trim72
authors E.Y.Park, O.B.Kwon, B.C.Jeong, H.K.Song
compound source
Molecule: Tripartite Motif-Containing Protein 72
Chain: A
Fragment: Pry-Spry Domain, Unp Residues 278-470
Synonym: Mitsugumin-53, Mg53
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Pry-Spry
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
symmetry Space Group: C 1 2 1
R_factor 0.219 R_Free 0.237
length a length b length c angle alpha angle beta angle gamma
153.747 35.937 33.200 90.00 99.87 90.00
method X-Ray Diffractionresolution 1.50 Å
note 3KB5 is a representative structure

Primary referenceCrystal structure of PRY-SPRY domain of human TRIM72., Park EY, Kwon OB, Jeong BC, Yi JS, Lee CS, Ko YG, Song HK, Proteins. 2009 Oct 30. PMID:19967786
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (38 Kb) [Save to disk]
  • Biological Unit Coordinates (3kb5.pdb1.gz) 34 Kb
  • Biological Unit Coordinates (3kb5.pdb2.gz) 68 Kb
  • CSU: Contacts of Structural Units for 3KB5
  • Structure Factors (326 Kb)
  • Retrieve 3KB5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3KB5 from S2C, [Save to disk]
  • Re-refined 3kb5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3KB5 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 3KB5
  • 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 3KB5, from MSDmotif at EBI
  • Fold representative 3kb5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3kb5_A] [3kb5]
  • SWISS-PROT database: [Q6ZMU5]
  • Belongs to the synaptosomal vesicle fusion pore (svf-pore) family according to TCDB.
  • Domain organization of [TRI72_HUMAN] by SWISSPFAM
  • Domains found in 3KB5: [PRY] [SPRY ] by SMART
  • Other resources with information on 3KB5
  • Community annotation for 3KB5 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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