2X29 Cell Adhesion date Jan 12, 2010
title Crystal Structure Of Human4-1bb Ligand Ectodomain
authors E.Y.Won, H.S.Cho
compound source
Molecule: Tumor Necrosis Factor Ligand Superfamily Member 9;
Chain: A
Fragment: Residues 80-246
Synonym: 4-1bb Ligand, 4-1bbl
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: B834(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 3 2 1
R_factor 0.21896 R_Free 0.23456
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.846 121.846 33.575 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.30 Å
ligand MSE enzyme
note 2X29 supersedes 2WAK
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structure of the trimer of human 4-1BB ligand is unique among members of the tumor necrosis factor superfamily., Won EY, Cha K, Byun JS, Kim DU, Shin S, Ahn B, Kim YH, Rice AJ, Walz T, Kwon BS, Cho HS, J Biol Chem. 2010 Mar 19;285(12):9202-10. Epub 2009 Dec 23. PMID:20032458
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (2x29.pdb1.gz) 76 Kb
  • LPC: Ligand-Protein Contacts for 2X29
  • CSU: Contacts of Structural Units for 2X29
  • Structure Factors (165 Kb)
  • Retrieve 2X29 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2X29 from S2C, [Save to disk]
  • Re-refined 2x29 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2X29 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 2X29
  • 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 2X29, from MSDmotif at EBI
  • Fold representative 2x29 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2x29] [2x29_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2X29: [TNF ] by SMART
  • Other resources with information on 2X29
  • Community annotation for 2X29 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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