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
crystal cell	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 Diffraction	resolution	2.80 Å
ligand	NAG	enzyme

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 (843 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 3IT8

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 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_A] [3it8_B] [3it8_C] [3it8_D] [3it8_E] [3it8_F] [3it8_G] [3it8_H] [3it8_I] [3it8_J] [3it8_K] [3it8_L] SWISS-PROT database: [Q9DHW0] [P01375] Domain organization of [Q9DHW0_YLDV] [TNFA_HUMAN] by SWISSPFAM Domains found in 3IT8: [IG_like] [TNF ] by SMART Alignments of the sequence of 3IT8 with the sequences similar proteins can be viewed for 3IT8's classification [Q9DHW0_YLDV] [TNFA_HUMAN] 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 [Q9DHW0_YLDV] [TNFA_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3IT8

Community annotation for 3IT8 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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