3ALQ Cytokine Cytokine Receptor date Aug 06, 2010
title Crystal Structure Of Tnf-Tnfr2 Complex
authors Y.Mukai, T.Nakamura, Y.Yamagata, Y.Tsutsumi
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C, D, E, F
Fragment: Soluble Form
Synonym: Tnf-Alpha, Tumor Necrosis Factor Ligand Superfamil 2, Tnf-A, Cachectin;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnf, Tnfa, Tnfsf2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pyas (Modified From Puc18)

Molecule: Tumor Necrosis Factor Receptor Superfamily Member
Chain: R, S, T, U, V, W
Fragment: Residues In Unp 33-205
Synonym: Tumor Necrosis Factor Receptor 2, Tnf-R2, Tumor Ne Factor-Binding Protein 2, Tbpii, Tbp-2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnfbr, Tnfr2, Tnfrsf1b
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pyas (Modified From Puc18)
symmetry Space Group: P 21 21 21
R_factor 0.213 R_Free 0.281
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.470 117.356 246.835 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand CO enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceSolution of the Structure of the TNF-TNFR2 Complex., Mukai Y, Nakamura T, Yoshikawa M, Yoshioka Y, Tsunoda S, Nakagawa S, Yamagata Y, Tsutsumi Y, Sci Signal. 2010 Nov 16;3(148):ra83. PMID:21081755
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (291 Kb) [Save to disk]
  • Biological Unit Coordinates (3alq.pdb1.gz) 145 Kb
  • Biological Unit Coordinates (3alq.pdb2.gz) 145 Kb
  • LPC: Ligand-Protein Contacts for 3ALQ
  • CSU: Contacts of Structural Units for 3ALQ
  • Structure Factors (294 Kb)
  • Retrieve 3ALQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ALQ from S2C, [Save to disk]
  • Re-refined 3alq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3ALQ 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 3ALQ
  • 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 3ALQ, from MSDmotif at EBI
  • Fold representative 3alq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3alq_F] [3alq_B] [3alq_T] [3alq_U] [3alq_V] [3alq_D] [3alq_W] [3alq_A] [3alq_S] [3alq_C] [3alq] [3alq_E] [3alq_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3ALQ: [TNF] [TNFR ] by SMART
  • Other resources with information on 3ALQ
  • Community annotation for 3ALQ 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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