3DJI	Isomerase	date	Jun 23, 2008
title	Crystal Structure Of Macrophage Migration Inhibitory Factor Bound To An Acetaminophen Dimer Derived From Napqi
authors	G.V.Crichlow, E.Lolis
compound		source
Molecule: Macrophage Migration Inhibitory Factor Chain: A, B, C, D, E, F Synonym: Mif, Phenylpyruvate Tautomerase, Glycosylation- Inhibiting Factor, Gif; Ec: 5.3.2.1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Gene: Mif, Glif, 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 1 21 1	R_factor 0.209 R_Free 0.247
crystal cell	length a length b length c angle alpha angle beta angle gamma 69.974 60.899 77.806 90.00 93.28 90.00
method	X-Ray Diffraction	resolution	1.95 Å
ligand	CL, TYL	enzyme	Isomerase E.C.5.3.2.1 BRENDA
Gene Ontology	Chain Function Process Component F, A, D, C, E, 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	Structural and Kinetic Analyses of Macrophage Migration Inhibitory Factor Active Site Interactions (dagger) (double dagger)., Crichlow GV, Lubetsky JB, Leng L, Bucala R, Lolis EJ, Biochemistry. 2008 Dec 17. PMID:19090677

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (116 Kb) [Save to disk] Biological Unit Coordinates (3dji.pdb1.gz) 58 Kb Biological Unit Coordinates (3dji.pdb2.gz) 57 Kb LPC: Ligand-Protein Contacts for 3DJI CSU: Contacts of Structural Units for 3DJI Likely Quarternary Molecular Structure file(s) for 3DJI Structure Factors (374 Kb) Retrieve 3DJI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3DJI from S2C, [Save to disk] Re-refined 3dji structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3DJI 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 3DJI

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

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3dji_A] [3dji_B] [3dji_C] [3dji_D] [3dji_E] [3dji_F] SWISS-PROT database: [P14174] Domain organization of [MIF_HUMAN] by SWISSPFAM Alignments of the sequence of 3DJI with the sequences similar proteins can be viewed for 3DJI's classification [MIF_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 [MIF_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 3DJI

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

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