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 Diffractionresolution 1.95 Å
ligand CL, TYL enzyme Isomerase E.C.5.3.2.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Primary referenceStructural 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 (376 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.
  • 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_E] [3dji_D] [3dji] [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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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