5LJN Ligase date Jul 18, 2016
title Structure Of The Hoip Pub Domain Bound To Spata2 Pim Peptide
authors P.R.Elliott, D.Komander
compound source
Molecule: E3 Ubiquitin-Protein Ligase Rnf31
Chain: A, B
Synonym: Hoil-1-Interacting Protein,Hoip,Ring Finger Protei In-Between-Ring-Finger Ubiquitin-Associated Domain Protein;
Ec: 6.3.2.-
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnf31, Zibra
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta II

Molecule: Spermatogenesis-Associated Protein 2
Chain: C, D
Fragment: Unp Residues 334-341
Synonym: Spermatogenesis-Associated Protein Pd1
Engineered: Yes

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 43
R_factor 0.233 R_Free 0.281
length a length b length c angle alpha angle beta angle gamma
89.040 89.040 53.563 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand GOL, SO4 enzyme Ligase E.C.6.3.2 BRENDA
A, B

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] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (5ljn.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (5ljn.pdb2.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 5LJN
  • CSU: Contacts of Structural Units for 5LJN
  • Structure Factors (706 Kb)
  • Retrieve 5LJN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5LJN from S2C, [Save to disk]
  • Re-refined 5ljn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5LJN 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 5LJN
  • 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
  • Fold representative 5ljn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ljn_B] [5ljn_D] [5ljn] [5ljn_A] [5ljn_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5LJN
  • Community annotation for 5LJN at PDBWiki (http://pdbwiki.org)

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