4N90 Apoptosis Immune System date Oct 18, 2013
title Crystal Structure Of Ternary Complex Of Trail, Dr5, And Fab From A Dr5 Agonist Antibody
authors X.Huang
compound source
Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: R, S, T
Fragment: Unp Residues 57-182
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: Tnfrsf10b, Dr5, Killer, Trailr2, Trick2, Ztnfr9, Unq160pro186;
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, C
Fragment: Unp Residues 114-281
Synonym: Apo-2 Ligand, Apo-2l, Tnf-Related Apoptosis-Induci 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: 562

Molecule: Fab Light Chain
Chain: E, G, I
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Fab Heavy Chain
Chain: D, F, H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: P 61 2 2
R_factor 0.229 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.006 152.006 613.155 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


S, T, R


Primary referenceApo2L/TRAIL and the Death Receptor 5 Agonist Antibody AMG 655 Cooperate to Promote Receptor Clustering and Antitumor Activity., Graves JD, Kordich JJ, Huang TH, Piasecki J, Bush TL, Sullivan T, Foltz IN, Chang W, Douangpanya H, Dang T, O'Neill JW, Mallari R, Zhao X, Branstetter DG, Rossi JM, Long AM, Huang X, Holland PM, Cancer Cell. 2014 Aug 11;26(2):177-89. doi: 10.1016/j.ccr.2014.04.028. Epub 2014 , Jul 17. PMID:25043603
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (334 Kb) [Save to disk]
  • Biological Unit Coordinates (4n90.pdb1.gz) 113 Kb
  • Biological Unit Coordinates (4n90.pdb2.gz) 113 Kb
  • Biological Unit Coordinates (4n90.pdb3.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 4N90
  • CSU: Contacts of Structural Units for 4N90
  • Structure Factors (1559 Kb)
  • Retrieve 4N90 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4N90 from S2C, [Save to disk]
  • Re-refined 4n90 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4N90 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 4N90
  • 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 4N90, from MSDmotif at EBI
  • Fold representative 4n90 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4n90_D] [4n90_A] [4n90_H] [4n90_I] [4n90_S] [4n90_G] [4n90_F] [4n90_R] [4n90_T] [4n90] [4n90_B] [4n90_E] [4n90_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4N90: [IG_like] [IGv] [TNF] [TNFR ] by SMART
  • Other resources with information on 4N90
  • Community annotation for 4N90 at PDBWiki (http://pdbwiki.org)

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