3X3F Apoptosis Immune System date Jan 20, 2015
title Trail-R2 Extracellular Region Complexed To A Fab Fragment Fr Agonist Antibody Kmtr2
authors T.Tamada
compound source
Molecule: Heavy Chain Of Kmtr2
Chain: H
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029

Molecule: Light Chain Of Kmtr2
Chain: L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: A
Fragment: Unp Residues 54-184
Synonym: Death Receptor 5, Tnf-Related Apoptosis-Inducing L Receptor 2, Trail Receptor 2, Trail-R2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dr5, Killer, Tnfrsf10b, Trailr2, Trick2, Unq160pro18 Ztnfr9;
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
symmetry Space Group: I 2 2 2
R_factor 0.186 R_Free 0.224
crystal
cell
length a length b length c angle alpha angle beta angle gamma
144.974 151.563 65.044 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand CL, GOL, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceTRAIL-R2 Superoligomerization Induced by Human Monoclonal Agonistic Antibody KMTR2., Tamada T, Shinmi D, Ikeda M, Yonezawa Y, Kataoka S, Kuroki R, Mori E, Motoki K, Sci Rep. 2015 Dec 17;5:17936. doi: 10.1038/srep17936. PMID:26672965
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (170 Kb) [Save to disk]
  • Biological Unit Coordinates (3x3f.pdb1.gz) 163 Kb
  • LPC: Ligand-Protein Contacts for 3X3F
  • CSU: Contacts of Structural Units for 3X3F
  • Structure Factors (805 Kb)
  • Retrieve 3X3F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3X3F from S2C, [Save to disk]
  • Re-refined 3x3f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3X3F 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 3X3F
  • 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 3x3f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3x3f] [3x3f_H] [3x3f_A] [3x3f_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3X3F: [IG_like] [IGv] [TNFR ] by SMART
  • Other resources with information on 3X3F
  • Community annotation for 3X3F at PDBWiki (http://pdbwiki.org)

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