5CIR Apoptosis date Jul 13, 2015
title Crystal Structure Of Death Receptor 4 (Dr4; Tnffrsf10a) Boun (Tnfsf10)
authors S.Sheriff
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, D
Fragment: Residues 114-281
Synonym: Apo-2 Ligand,Apo-2l,Tnf-Related Apoptosis-Inducing Protein Trail;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfsf10, Apo2l, Trail
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28-Nhis-Tev

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: E, F, G
Fragment: Extracellular Domain Residues 125-232
Synonym: Death Receptor 4,Tnf-Related Apoptosis-Inducing Li Receptor 1,Trail-R1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf10a, Apo2, Dr4, Trailr1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Oragami B(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28
symmetry Space Group: P 21 21 21
R_factor 0.177 R_Free 0.216
crystal
cell
length a length b length c angle alpha angle beta angle gamma
84.600 87.600 107.700 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CL, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, B


F, G, E


Primary referenceThe structure of the death receptor 4-TNF-related apoptosis-inducing ligand (DR4-TRAIL) complex., Ramamurthy V, Yamniuk AP, Lawrence EJ, Yong W, Schneeweis LA, Cheng L, Murdock M, Corbett MJ, Doyle ML, Sheriff S, Acta Crystallogr F Struct Biol Commun. 2015 Oct;71(Pt 10):1273-81. doi:, 10.1107/S2053230X15016416. Epub 2015 Sep 23. PMID:26457518
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (121 Kb) [Save to disk]
  • Biological Unit Coordinates (5cir.pdb1.gz) 115 Kb
  • LPC: Ligand-Protein Contacts for 5CIR
  • CSU: Contacts of Structural Units for 5CIR
  • Structure Factors (176 Kb)
  • Retrieve 5CIR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5CIR from S2C, [Save to disk]
  • Re-refined 5cir structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5CIR 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 5CIR
  • 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 5cir from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5cir_G] [5cir_B] [5cir_E] [5cir] [5cir_F] [5cir_D] [5cir_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5CIR
  • Community annotation for 5CIR at PDBWiki (http://pdbwiki.org)

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