1D0G Apoptosis date Sep 09, 1999
title Crystal Structure Of Death Receptor 5 (Dr5) Bound To Apo2ltrail
authors S.G.Hymowitz, H.W.Christinger, G.Fuh, M.P.O'Connell, R.F.Kelley, A.Ashkenazi, A.M.De Vos
compound source
Molecule: Death Receptor-5
Chain: R, S, T
Fragment: Extracellular Domain Residues 1-130
Synonym: Dr-5
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Unidentified Baculovirus
Expression_system_taxid: 10469
Expression_system_vector: Baculovirus With Polyhedrin Promoter;

Molecule: Apoptosis-2 Ligand
Chain: A, B, D
Fragment: Residues 114-281
Synonym: Trail, Apo2l
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Bacteria
Expression_system_common: Eubacteria
Expression_system_taxid: 2
Expression_system_vector: Ap Promoter
symmetry Space Group: P 21 21 21
R_factor 0.222 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.818 111.019 130.807 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand CL, ZN enzyme
related structures by homologous chain: 1D2Q, 1DU3
Gene
Ontology
ChainFunctionProcessComponent
A, D, B


S, T, R


Primary referenceTriggering cell death: the crystal structure of Apo2L/TRAIL in a complex with death receptor 5., Hymowitz SG, Christinger HW, Fuh G, Ultsch M, O'Connell M, Kelley RF, Ashkenazi A, de Vos AM, Mol Cell 1999 Oct;4(4):563-71. PMID:10549288
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (139 Kb) [Save to disk]
  • Biological Unit Coordinates (1d0g.pdb1.gz) 133 Kb
  • LPC: Ligand-Protein Contacts for 1D0G
  • CSU: Contacts of Structural Units for 1D0G
  • Likely Quarternary Molecular Structure file(s) for 1D0G
  • Structure Factors (320 Kb)
  • Retrieve 1D0G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D0G from S2C, [Save to disk]
  • Re-refined 1d0g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D0G 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 1D0G
  • 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
  • 3D motif for 1D0G, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d0ga_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1d0gb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1d0gd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1d0gr3, region R:102-128 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gr1, region R:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gr2, region R:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gs3, region S:102-130 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gs1, region S:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gs2, region S:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gt3, region T:102-130 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gt1, region T:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1d0gt2, region T:62-101 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d0g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1d0g_T] [1d0g_D] [1d0g] [1d0g_S] [1d0g_A] [1d0g_R] [1d0g_B]
  • SWISS-PROT database: [P50591] [O14763]
  • Domain organization of [TNF10_HUMAN] [TR10B_HUMAN] by SWISSPFAM
  • Domains found in 1D0G: [TNF] [TNFR ] by SMART
  • Other resources with information on 1D0G
  • Community annotation for 1D0G 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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