3IMX Transferase date Aug 11, 2009
title Crystal Structure Of Human Glucokinase In Complex With A Synthetic Activator
authors T.Stams, B.Vash
compound source
Molecule: Glucokinase
Chain: A
Fragment: Residues 16-465
Synonym: Hexokinase 4, Maturity Onset Diabetes Of The Young 2, Isoform Cra_b;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gck, Hcg_1745191, Tcag7.801
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
symmetry Space Group: P 21 21 21
R_factor 0.195 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
45.500 90.300 116.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand B84, GLC, NA enzyme
Gene HCG
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceInvestigation of functionally liver selective glucokinase activators for the treatment of type 2 diabetes., Bebernitz GR, Beaulieu V, Dale BA, Deacon R, Duttaroy A, Gao J, Grondine MS, Gupta RC, Kakmak M, Kavana M, Kirman LC, Liang J, Maniara WM, Munshi S, Nadkarni SS, Schuster HF, Stams T, St Denny I, Taslimi PM, Vash B, Caplan SL, J Med Chem. 2009 Oct 8;52(19):6142-52. PMID:19746978
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (82 Kb) [Save to disk]
  • Biological Unit Coordinates (3imx.pdb1.gz) 78 Kb
  • LPC: Ligand-Protein Contacts for 3IMX
  • CSU: Contacts of Structural Units for 3IMX
  • Structure Factors (834 Kb)
  • Retrieve 3IMX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IMX from S2C, [Save to disk]
  • Re-refined 3imx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3IMX 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 3IMX
  • 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 3IMX, from MSDmotif at EBI
  • Fold representative 3imx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3imx_A] [3imx]
  • SWISS-PROT database: [P35557]
  • Domain organization of [HXK4_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 3IMX with the sequences similar proteins can be viewed for 3IMX's classification [HXK4_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 [HXK4_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3IMX
  • Community annotation for 3IMX 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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