1U5Y Cytokine, Hormone Growth Factor date Jul 28, 2004
title Crystal Structure Of Murine April, Ph 8.0
authors H.J.Wallweber, D.M.Compaan, M.A.Starovasnik, S.G.Hymowitz
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 1
Chain: A, B, D
Fragment: Tnf Domain Of Murine April
Synonym: A Proliferation- Inducing Ligand, April
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Tnfsf13, April
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-32a (Modified)
symmetry Space Group: C 1 2 1
R_factor 0.201 R_Free 0.268
length a length b length c angle alpha angle beta angle gamma
123.344 81.166 53.585 90.00 111.79 90.00
method X-Ray Diffractionresolution 2.30 Å
related structures by homologous chain: 1XU1, 1XU2
Primary referenceThe Crystal Structure of A Proliferation-inducing Ligand, APRIL., Wallweber HJ, Compaan DM, Starovasnik MA, Hymowitz SG, J Mol Biol 2004 Oct 15;343(2):283-90. PMID:15451660
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (71 Kb) [Save to disk]
  • Biological Unit Coordinates (1u5y.pdb1.gz) 65 Kb
  • CSU: Contacts of Structural Units for 1U5Y
  • Likely Quarternary Molecular Structure file(s) for 1U5Y
  • Structure Factors (152 Kb)
  • Retrieve 1U5Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U5Y from S2C, [Save to disk]
  • Re-refined 1u5y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1U5Y 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 1U5Y
  • 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 1U5Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u5ya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1u5yb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1u5yd_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1u5y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1u5y_D] [1u5y_A] [1u5y_B] [1u5y]
  • SWISS-PROT database: [Q9D777]
  • Domain organization of [TNF13_MOUSE] by SWISSPFAM
  • Domain found in 1U5Y: [TNF ] by SMART
  • Other resources with information on 1U5Y
  • Community annotation for 1U5Y 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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