5LJM Cell Cycle date Jul 18, 2016
title Structure Of Spata2 Pub Domain
authors P.R.Elliott, D.Komander
compound source
Molecule: Spermatogenesis-Associated Protein 2
Chain: A
Synonym: Spermatogenesis-Associated Protein Pd1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Spata2, Kiaa0757, Pd1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta II
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popink
symmetry Space Group: P 1 21 1
R_factor 0.182 R_Free 0.225
length a length b length c angle alpha angle beta angle gamma
43.480 51.140 56.290 90.00 105.97 90.00
method X-Ray Diffractionresolution 1.45 Å
ligand GOL enzyme
Primary referenceSPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling., Elliott PR, Leske D, Hrdinka M, Bagola K, Fiil BK, McLaughlin SH, Wagstaff J, Volkmar N, Christianson JC, Kessler BM, Freund SM, Komander D, Gyrd-Hansen M, Mol Cell. 2016 Aug 27. pii: S1097-2765(16)30415-4. doi:, 10.1016/j.molcel.2016.08.001. PMID:27591049
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (5ljm.pdb1.gz) 77 Kb
  • LPC: Ligand-Protein Contacts for 5LJM
  • CSU: Contacts of Structural Units for 5LJM
  • Structure Factors (2469 Kb)
  • Retrieve 5LJM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LJM from S2C, [Save to disk]
  • Re-refined 5ljm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LJM 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 5LJM
  • 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
  • Fold representative 5ljm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ljm_A] [5ljm]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5LJM
  • Community annotation for 5LJM at PDBWiki (http://pdbwiki.org)

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