3IT8 Immune System date Aug 27, 2009
title Crystal Structure Of Tnf Alpha Complexed With A Poxvirus Mhc Tnf Binding Protein
authors Z.Yang, A.P.West Jr., P.J.Bjorkman
compound source
Molecule: Tumor Necrosis Factor
Chain: A, B, C, G, H, I
Fragment: Tumor Necrosis Factor, Soluble Form, Unp Residues
Synonym: Tnf-Alpha, Tumor Necrosis Factor Ligand Superfamil 2, Tnf-A, Cachectin, Tumor Necrosis Factor, Membrane Form, Necrosis Factor, Soluble Form;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tnf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23a

Molecule: 2l Protein
Chain: D, E, F, J, K, L
Engineered: Yes

Organism_scientific: Yaba-Like Disease Virus
Organism_common: Yldv
Organism_taxid: 132475
Strain: Atcc Vr-937
Gene: 2l
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Cell_line: Bti-Tn-5b1-4
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pacuw31
symmetry Space Group: P 1 21 1
R_factor 0.236 R_Free 0.266
length a length b length c angle alpha angle beta angle gamma
101.656 170.295 122.002 90.00 92.04 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand NAG enzyme
A, B, H, C, I, G

F, J, K, E, D, L
  • protein serine/threonine kin...

  • Primary referenceCrystal structure of TNFalpha complexed with a poxvirus MHC-related TNF binding protein., Yang Z, West AP Jr, Bjorkman PJ, Nat Struct Mol Biol. 2009 Nov;16(11):1189-91. Epub 2009 Oct 18. PMID:19838188
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (436 Kb) [Save to disk]
  • Biological Unit Coordinates (3it8.pdb1.gz) 217 Kb
  • Biological Unit Coordinates (3it8.pdb2.gz) 217 Kb
  • LPC: Ligand-Protein Contacts for 3IT8
  • CSU: Contacts of Structural Units for 3IT8
  • Structure Factors (848 Kb)
  • Retrieve 3IT8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IT8 from S2C, [Save to disk]
  • Re-refined 3it8 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IT8 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 3IT8
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  • 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 3IT8, from MSDmotif at EBI
  • Fold representative 3it8 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3it8_D] [3it8_A] [3it8_I] [3it8_H] [3it8_J] [3it8_C] [3it8_E] [3it8_K] [3it8_L] [3it8_G] [3it8] [3it8_B] [3it8_F]
  • SWISS-PROT database: [Q9DHW0] [P01375]
  • Domain organization of [Q9DHW0_YLDV] [TNFA_HUMAN] by SWISSPFAM
  • Domains found in 3IT8: [IG_like] [TNF ] by SMART
  • Other resources with information on 3IT8
  • Community annotation for 3IT8 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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