3L9J	Immune System	date	Jan 05, 2010
title	Selection Of A Novel Highly Specific Tnfalpha Antagonist: Insight From The Crystal Structure Of The Antagonist- Tnfalpha Complex
authors	P.Byla, M.H.Andersen, H.C.Thogersen, H.H.Gad, R.Hartmann
compound		source
Molecule: Tnfalpha Chain: C Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7ciih6
Molecule: Tumor Necrosis Factor, Soluble Form Chain: T Fragment: Unp Residues 85-233 Synonym: Tnf-Alpha, Tumor Necrosis Factor Ligand Superfamily Member 2, Tnf-A, Cachectin; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pt7ciih6
symmetry	Space Group: P 63 2 2	R_factor 0.173 R_Free 0.217
crystal cell	length a length b length c angle alpha angle beta angle gamma 83.905 83.905 149.172 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.10 Å
ligand	MG	enzyme
Primary reference	Selection of a novel and highly specific tumor necrosis factor alpha (TNFalpha) antagonist: insight from the crystal structure of the antagonist-TNFalpha complex., Byla P, Andersen MH, Holtet TL, Jacobsen H, Munch M, Gad HH, Thogersen HC, Hartmann R, J Biol Chem. 2010 Apr 16;285(16):12096-100. Epub 2010 Feb 23. PMID:20179326

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (56 Kb) [Save to disk] Biological Unit Coordinates (3l9j.pdb1.gz) 25 Kb Biological Unit Coordinates (3l9j.pdb2.gz) 28 Kb LPC: Ligand-Protein Contacts for 3L9J CSU: Contacts of Structural Units for 3L9J Structure Factors (257 Kb) Retrieve 3L9J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3L9J from S2C, [Save to disk] Re-refined 3l9j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3L9J 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 3L9J

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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 3L9J, from MSDmotif at EBI Fold representative 3l9j from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3l9j_C] [3l9j_T] SWISS-PROT database: Domain organization of by SWISSPFAM Alignments of the sequence of 3L9J with the sequences similar proteins can be viewed for 3L9J'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 3L9J

Community annotation for 3L9J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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