1U5Z Cytokine, Hormone Growth Factor date Jul 28, 2004
title The Crystal Structure Of Murine April, Ph 8.5
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
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: I 2 3
R_factor 0.219 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.166 92.166 92.166 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NI enzyme
related structures by homologous chain: 1XU2
Gene
Ontology
ChainFunctionProcessComponent
A


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] (26 Kb) [Save to disk]
  • Biological Unit Coordinates (1u5z.pdb1.gz) 61 Kb
  • LPC: Ligand-Protein Contacts for 1U5Z
  • CSU: Contacts of Structural Units for 1U5Z
  • Likely Quarternary Molecular Structure file(s) for 1U5Z
  • Structure Factors (41 Kb)
  • Retrieve 1U5Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U5Z from S2C, [Save to disk]
  • Re-refined 1u5z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1U5Z 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 1U5Z
  • 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 1U5Z, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u5za_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1u5z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1u5z] [1u5z_A]
  • SWISS-PROT database: [Q9D777]
  • Domain organization of [TNF13_MOUSE] by SWISSPFAM
  • Domain found in 1U5Z: [TNF ] by SMART
  • Other resources with information on 1U5Z
  • Community annotation for 1U5Z 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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