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- PDB-1hkg: STRUCTURAL DYNAMICS OF YEAST HEXOKINASE DURING CATALYSIS -

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Basic information

Entry
Database: PDB / ID: 1hkg
TitleSTRUCTURAL DYNAMICS OF YEAST HEXOKINASE DURING CATALYSIS
ComponentsHEXOKINASE A
KeywordsTRANSFERASE
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / fructose import across plasma membrane / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / fructose import across plasma membrane / hexokinase activity / Glycolysis / mannokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / D-glucose binding / fructose metabolic process / D-glucose import / intracellular glucose homeostasis / Neutrophil degranulation / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. ...Helix Hairpins - #1250 / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Helix Hairpins / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsBennett Jr., W.S. / Steitz, T.A.
Citation
Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: Structural dynamics of yeast hexokinase during catalysis.
Authors: Steitz, T.A. / Shoham, M. / Bennett Jr., W.S.
#1: Journal: J.Mol.Biol. / Year: 1980
Title: Structure of a complex between yeast hexokinase A and glucose. II. Detailed comparisons of conformation and active site configuration with the native hexokinase B monomer and dimer.
Authors: Bennett Jr., W.S. / Steitz, T.A.
#2: Journal: J.Mol.Biol. / Year: 1980
Title: Structure of a complex between yeast hexokinase A and glucose. I. Structure determination and refinement at 3.5 A resolution.
Authors: Bennett Jr., W.S. / Steitz, T.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Glucose-induced conformational change in yeast hexokinase.
Authors: Bennett Jr., W.S. / Steitz, T.A.
History
DepositionDec 22, 1980Processing site: BNL
Revision 1.0Feb 26, 1981Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 25, 2012Group: Database references / Structure summary
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEXOKINASE A


Theoretical massNumber of molelcules
Total (without water)46,0251
Polymers46,0251
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.800, 78.800, 61.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUE DENOTED *GAM* BY DEPOSITOR. / 2: RESIDUE DENOTED *DEL* BY DEPOSITOR. / 3: RESIDUE DENOTED *EPS* BY DEPOSITOR.

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Components

#1: Protein HEXOKINASE A


Mass: 46024.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P04806*PLUS, hexokinase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.93 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 3.5 Å
Refinement stepCycle: LAST / Highest resolution: 3.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3298 0 0 0 3298

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