3IJJ	Isomerase	date	Aug 04, 2009
title	Ternary Complex Of Macrophage Migration Inhibitory Factor (M Both To 4-Hydroxyphenylpyruvate And To The Allosteric Inhib Av1013 (R-Stereoisomer)
authors	G.V.Crichlow, Y.Cho, E.J.Lolis
compound		source
Molecule: Macrophage Migration Inhibitory Factor Chain: A, B, C Synonym: Mif, Phenylpyruvate Tautomerase, L-Dopachrome Taut L-Dopachrome Isomerase, Glycosylation-Inhibiting Factor, Gi Ec: 5.3.2.1, 5.3.3.12 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Glif, Mif, Mmif Expression_system: Escherichia Coli Expression_system_taxid: 562 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet11b
symmetry	Space Group: P 21 21 21	R_factor 0.162 R_Free 0.185
crystal cell	length a length b length c angle alpha angle beta angle gamma 67.236 67.908 87.329 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	1.25 Å
ligand	AVR, CL, EN1, ENO	enzyme	Isomerase E.C.5.3.2.1 BRENDA
Gene Ontology	Chain Function Process Component A, C, B dopachrome isomerase activit... receptor binding cytokine activity cytokine receptor binding protein binding isomerase activity chemoattractant activity cell surface binding phenylpyruvate tautomerase a... prostaglandin biosynthetic p... positive regulation of prote... negative regulation of matur... inflammatory response cell surface receptor signal... cell aging cell proliferation negative regulation of gene ... positive regulation of prote... carboxylic acid metabolic pr... DNA damage response, signal ... positive regulation of B cel... positive regulation of lipop... negative regulation of cellu... negative regulation of myelo... positive regulation of pepti... regulation of cell prolifera... positive regulation of phosp... regulation of macrophage act... negative regulation of apopt... positive regulation of MAP k... negative regulation of DNA d... innate immune response positive regulation of fibro... positive regulation of cytok... positive regulation of pepti... positive chemotaxis positive regulation of prost... positive regulation of myelo... protein homotrimerization positive regulation of ERK1 ... negative regulation of cell ... positive regulation of arach... negative regulation of cell ... positive regulation of chemo... extracellular region extracellular space cytoplasm cell surface
Primary reference	Allosteric inhibition of macrophage migration inhibitory factor revealed by ibudilast., Cho Y, Crichlow GV, Vermeire JJ, Leng L, Du X, Hodsdon ME, Bucala R, Cappello M, Gross M, Gaeta F, Johnson K, Lolis EJ, Proc Natl Acad Sci U S A. 2010 Jun 22;107(25):11313-8. Epub 2010 Jun 8. PMID:20534506

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk] Biological Unit Coordinates (3ijj.pdb1.gz) 125 Kb LPC: Ligand-Protein Contacts for 3IJJ CSU: Contacts of Structural Units for 3IJJ Structure Factors (1380 Kb) Retrieve 3IJJ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3IJJ from S2C, [Save to disk] Re-refined 3ijj structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3IJJ 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 3IJJ

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

Sequence-derived information

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

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

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