6D3N Signaling Protein date Apr 16, 2018
title Crystal Structure Of H4-1bb Ligand
authors B.Aruna, D.M.Zajonc, T.Doukov
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 9
Chain: A
Fragment: Residues 80-244
Synonym: 4-1bb Ligand,4-1bbl
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfsf9
Expression_system: Insect Cell Expression Vector Ptie1
Expression_system_taxid: 266783
symmetry Space Group: H 3 2
R_factor 0.208 R_Free 0.252
length a length b length c angle alpha angle beta angle gamma
73.167 73.167 162.814 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
ligand GOL enzyme

Primary referenceCrystal structures of the human 4-1BB receptor bound to its ligand 4-1BBL reveal covalent receptor dimerization as a potential signaling amplifier., Bitra A, Doukov T, Croft M, Zajonc DM, J Biol Chem. 2018 May 2. pii: RA118.003176. doi: 10.1074/jbc.RA118.003176. PMID:29720398
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (6d3n.pdb1.gz) 63 Kb
  • LPC: Ligand-Protein Contacts for 6D3N
  • CSU: Contacts of Structural Units for 6D3N
  • Structure Factors (139 Kb)
  • Retrieve 6D3N in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D3N from S2C, [Save to disk]
  • View 6D3N 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 6D3N
  • 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 6d3n from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d3n_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6D3N
  • Community annotation for 6D3N 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
    Bioinformatics Unit
    Weizmann Institute of Science