1DGK Transferase date Nov 24, 1999
title Mutant Monomer Of Recombinant Human Hexokinase Type I With Glucose And Adp In The Active Site
authors A.E.Aleshin, X.Liu, C.Kirby, G.P.Bourenkov, H.D.Bartunik, H.J.Fromm, R.B.Honzatko
compound source
Molecule: Hexokinase Type I
Chain: N
Synonym: Hk I, Brain Form Hexokinase
Ec: 2.7.1.1
Engineered: Yes
Mutation: Yes
Other_details: Second Molecule Of Adp Is Bound Near The N- Terminus Of The Polypeptide Chain. The Regulatory Site Of The N-Terminal Domain Is Occupied With Glucose And Phosphate. Mutations In Dimer Interface And The Active Site
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Brain
Cell: Neuron
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 21 21 2
R_factor 0.258 R_Free 0.308
crystal
cell
length a length b length c angle alpha angle beta angle gamma
145.780 146.830 58.590 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ADP, GLC, PO4 enzyme Transferase E.C.2.7.1.1 BRENDA
note 1DGK (Molecule of the Month:pdb50)
related structures by homologous chain: 1HKB
Gene
Ontology
ChainFunctionProcessComponent
N


Primary referenceCrystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation., Aleshin AE, Kirby C, Liu X, Bourenkov GP, Bartunik HD, Fromm HJ, Honzatko RB, J Mol Biol 2000 Mar 3;296(4):1001-15. PMID:10686099
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (153 Kb) [Save to disk]
  • Biological Unit Coordinates (1dgk.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 1DGK
  • CSU: Contacts of Structural Units for 1DGK
  • Likely Quarternary Molecular Structure file(s) for 1DGK
  • Structure Factors (231 Kb)
  • Retrieve 1DGK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1DGK from S2C, [Save to disk]
  • Re-refined 1dgk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1DGK 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 1DGK
  • 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 1DGK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1dgkn1, region N:16-222 [Jmol] [rasmolscript] [script source]
        - Domain d1dgkn2, region N:223-465 [Jmol] [rasmolscript] [script source]
        - Domain d1dgkn3, region N:466-670 [Jmol] [rasmolscript] [script source]
        - Domain d1dgkn4, region N:671-913 [Jmol] [rasmolscript] [script source]
  • Fold representative 1dgk from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1dgk_N] [1dgk]
  • SWISS-PROT database: [P19367]
  • Domain organization of [HXK1_HUMAN] by SWISSPFAM
  • Alignments of the sequence of 1DGK with the sequences similar proteins can be viewed for 1DGK's classification [HXK1_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 [HXK1_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1DGK
  • Community annotation for 1DGK 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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