1DU3 Apoptosis date Jan 14, 2000
title Crystal Structure Of Trail-Sdr5
authors S.S.Cha, B.J.Sung, B.H.Oh
compound source
Molecule: Death Receptor 5
Chain: A, B, C, G, H, I
Fragment: Extracellular Domain
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Tnf-Related Apoptosis Inducing Ligand
Chain: D, E, F, J, K, L
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Bacteria
Expression_system_common: Eubacteria
Expression_system_taxid: 2
symmetry Space Group: P 1 21 1
R_factor 0.291 R_Free 0.291
crystal
cell
length a length b length c angle alpha angle beta angle gamma
68.630 124.810 128.370 90.00 104.49 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand ZN enzyme
related structures by homologous chain: 1D0G, 1D4V
Gene
Ontology
ChainFunctionProcessComponent
A, B, H, C, I, G


F, J, K, E, D, L


Primary referenceCrystal structure of TRAIL-DR5 complex identifies a critical role of the unique frame insertion in conferring recognition specificity., Cha SS, Sung BJ, Kim YA, Song YL, Kim HJ, Kim S, Lee MS, Oh BH, J Biol Chem 2000 Oct 6;275(40):31171-7. PMID:10893238
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (254 Kb) [Save to disk]
  • Biological Unit Coordinates (1du3.pdb1.gz) 124 Kb
  • Biological Unit Coordinates (1du3.pdb2.gz) 125 Kb
  • LPC: Ligand-Protein Contacts for 1DU3
  • CSU: Contacts of Structural Units for 1DU3
  • Likely Quarternary Molecular Structure file(s) for 1DU3
  • Retrieve 1DU3 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DU3 from S2C, [Save to disk]
  • View 1DU3 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 1DU3
  • 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 1DU3, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1du3a3, region A:102-123 [Jmol] [rasmolscript] [script source]
        - Domain d1du3a1, region A:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1du3a2, region A:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1du3b3, region B:102-130 [Jmol] [rasmolscript] [script source]
        - Domain d1du3b1, region B:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1du3b2, region B:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1du3c3, region C:102-123 [Jmol] [rasmolscript] [script source]
        - Domain d1du3c1, region C:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1du3c2, region C:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1du3d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1du3e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1du3f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1du3g3, region G:102-128 [Jmol] [rasmolscript] [script source]
        - Domain d1du3g1, region G:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1du3g2, region G:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1du3h3, region H:102-123 [Jmol] [rasmolscript] [script source]
        - Domain d1du3h1, region H:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1du3h2, region H:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1du3i3, region I:102-123 [Jmol] [rasmolscript] [script source]
        - Domain d1du3i1, region I:21-61 [Jmol] [rasmolscript] [script source]
        - Domain d1du3i2, region I:62-101 [Jmol] [rasmolscript] [script source]
        - Domain d1du3j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1du3k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1du3l_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1du3 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: [1du3_C] [1du3_I] [1du3_H] [1du3_K] [1du3_F] [1du3_G] [1du3] [1du3_D] [1du3_J] [1du3_E] [1du3_A] [1du3_B] [1du3_L]
  • SWISS-PROT database: [P50591] [O14763]
  • Domain organization of [TNF10_HUMAN] [TR10B_HUMAN] by SWISSPFAM
  • Domains found in 1DU3: [TNF] [TNFR ] by SMART
  • Alignments of the sequence of 1DU3 with the sequences similar proteins can be viewed for 1DU3'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 1DU3
  • Community annotation for 1DU3 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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