2H9G Immune System Apoptosis date Jun 09, 2006
title Crystal Structure Of Phage Derived Fab Bdf1 With Human Death (Dr5)
authors S.G.Hymowitz, D.M.Compaan
compound source
Molecule: Fab Bdf1, Light Chain
Chain: A, L
Fragment: Fab Fragment
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Protein Selected By Phage Display

Molecule: Fab Bdf1, Heavy Chain
Chain: B, H
Fragment: Fab Fragment
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Protein Selected By Phage Display

Molecule: Tumor Necrosis Factor Receptor Superfamily Member Precursor;
Chain: R, S
Fragment: Extra Cellular Domain
Synonym: Death Receptor 5, Tnf-Related Apoptosis-Inducing L Receptor 2, Trail Receptor 2, Trail-R2, Cd262 Antigen;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfrsf10b, Dr5, Killer, Trailr2, Trick2, Ztnfr9
Expression_system: Spodoptera Frugiperda
Expression_system_common: Fall Armyworm
Expression_system_taxid: 7108
Expression_system_strain: Hi5
Expression_system_vector_type: Virus
Expression_system_plasmid: Pacgp67-B
symmetry Space Group: P 1 21 1
R_factor 0.228 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.814 61.389 108.269 90.00 101.17 90.00
method X-Ray Diffractionresolution 2.32 Å
Gene
Ontology
ChainFunctionProcessComponent
S, R


Primary referenceActivation of the Proapoptotic Death Receptor DR5 by Oligomeric Peptide and Antibody Agonists., Li B, Russell SJ, Compaan DM, Totpal K, Marsters SA, Ashkenazi A, Cochran AG, Hymowitz SG, Sidhu SS, J Mol Biol. 2006 Aug 18;361(3):522-36. Epub 2006 Jul 7. PMID:16859704
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (2h9g.pdb1.gz) 86 Kb
  • Biological Unit Coordinates (2h9g.pdb2.gz) 78 Kb
  • CSU: Contacts of Structural Units for 2H9G
  • Likely Quarternary Molecular Structure file(s) for 2H9G
  • Structure Factors (756 Kb)
  • Retrieve 2H9G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2H9G from S2C, [Save to disk]
  • Re-refined 2h9g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2H9G 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 2H9G
  • 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
  • 3D motif for 2H9G, from MSDmotif at EBI
  • Fold representative 2h9g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2h9g_L] [2h9g_H] [2h9g_R] [2h9g_S] [2h9g_B] [2h9g] [2h9g_A]
  • SWISS-PROT database: [O14763]
  • Domain organization of [TR10B_HUMAN] by SWISSPFAM
  • Domains found in 2H9G: [IGc1] [IGv] [TNFR ] by SMART
  • Other resources with information on 2H9G
  • Community annotation for 2H9G at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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