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
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
  • Alignments of the sequence of 3ALQ with the sequences similar proteins can be viewed for 3ALQ's classification 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 at ProtoMap. Click on the Cluster number.
  • 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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