1D4V Apoptosis date Oct 06, 1999
title Crystal Structure Of Trail-Dr5 Complex
authors J.Mongkolsapaya, J.M.Grimes, D.I.Stuart, E.Y.Jones, G.R.Screaton
compound source
Molecule: Tnf-Related Apoptosis Inducing Ligand
Chain: B
Fragment: Single Subunit
Synonym: Trail
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-9c

Molecule: Death Receptor 5
Chain: A
Fragment: Extracellular Region
Synonym: Dr5
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Transient Expression As Ig Fusion Protein
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell: 293t Cells
symmetry Space Group: P 3 2 1
R_factor 0.221 R_Free 0.270
crystal
cell
length a length b length c angle alpha angle beta angle gamma
95.520 95.520 69.810 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
note 1D4V is a representative structure
related structures by homologous chain: 1DG6, 1DU3
Primary referenceStructure of the TRAIL-DR5 complex reveals mechanisms conferring specificity in apoptotic initiation., Mongkolsapaya J, Grimes JM, Chen N, Xu XN, Stuart DI, Jones EY, Screaton GR, Nat Struct Biol. 1999 Nov;6(11):1048-53. PMID:10542098
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (54 Kb) [Save to disk]
  • Biological Unit Coordinates (1d4v.pdb1.gz) 146 Kb
  • CSU: Contacts of Structural Units for 1D4V
  • Likely Quarternary Molecular Structure file(s) for 1D4V
  • Retrieve 1D4V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D4V from S2C, [Save to disk]
  • View 1D4V 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 1D4V
  • 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 1D4V, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d4va2, region A:115-154 [Jmol] [rasmolscript] [script source]
        - Domain d1d4va3, region A:155-185 [Jmol] [rasmolscript] [script source]
        - Domain d1d4va1, region A:69-114 [Jmol] [rasmolscript] [script source]
        - Domain d1d4vb_, region B [Jmol] [rasmolscript] [script source]
  • Fold representative 1d4v 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: [1d4v] [1d4v_A] [1d4v_B]
  • SWISS-PROT database: [P50591] [O14763]
  • Domain organization of [TNF10_HUMAN] [TR10B_HUMAN] by SWISSPFAM
  • Domains found in 1D4V: [TNF] [TNFR ] by SMART
  • Alignments of the sequence of 1D4V with the sequences similar proteins can be viewed for 1D4V's classification [TNF10_HUMAN] [TR10B_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [TNF10_HUMAN] [TR10B_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1D4V
  • Community annotation for 1D4V 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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