2ICK Isomerase date Sep 12, 2006
title Human Isopentenyl Diphophate Isomerase Complexed With Substr
authors W.Zheng, M.Bartlam, Z.Rao
compound source
Molecule: Isopentenyl-Diphosphate Delta Isomerase
Chain: A
Synonym: Idi1 Protein
Ec: 5.3.3.2
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: Pgex-6p
symmetry Space Group: P 21 21 21
R_factor 0.205 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.812 47.396 116.817 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.93 Å
ligand DMA, MN enzyme Isomerase E.C.5.3.3.2 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis., Zheng W, Sun F, Bartlam M, Li X, Li R, Rao Z, J Mol Biol. 2007 Mar 9;366(5):1447-58. Epub 2006 Dec 24. PMID:17250851
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (44 Kb) [Save to disk]
  • Biological Unit Coordinates (2ick.pdb1.gz) 40 Kb
  • LPC: Ligand-Protein Contacts for 2ICK
  • CSU: Contacts of Structural Units for 2ICK
  • Likely Quarternary Molecular Structure file(s) for 2ICK
  • Structure Factors (266 Kb)
  • Retrieve 2ICK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ICK from S2C, [Save to disk]
  • Re-refined 2ick structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2ICK 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 2ICK
  • 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
  • 3D motif for 2ICK, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ick_A] [2ick]
  • SWISS-PROT database: [Q13907]
  • Domain organization of [IDI1_HUMAN] by SWISSPFAM
  • Other resources with information on 2ICK
  • Community annotation for 2ICK 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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