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- PDB-1bg3: RAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GL... -

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Basic information

Entry
Database: PDB / ID: 1bg3
TitleRAT BRAIN HEXOKINASE TYPE I COMPLEX WITH GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE
ComponentsHEXOKINASE
KeywordsHEXOKINASE / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


response to ketamine / Glycolysis / regulation of anion channel activity / response to brassinosteroid / sperm principal piece / hexokinase activity / maintenance of protein location in mitochondrion / carbohydrate phosphorylation / positive regulation of cytokine production involved in immune response / mannokinase activity ...response to ketamine / Glycolysis / regulation of anion channel activity / response to brassinosteroid / sperm principal piece / hexokinase activity / maintenance of protein location in mitochondrion / carbohydrate phosphorylation / positive regulation of cytokine production involved in immune response / mannokinase activity / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / glucokinase activity / glucose 6-phosphate metabolic process / mannose metabolic process / peptidoglycan binding / glucose binding / fructose 6-phosphate metabolic process / cellular glucose homeostasis / response to ischemia / positive regulation of interleukin-1 beta production / caveola / cilium / glycolytic process / peptidyl-tyrosine phosphorylation / peptidyl-threonine phosphorylation / mitochondrial outer membrane / response to hypoxia / peptidyl-serine phosphorylation / protein kinase activity / inflammatory response / protein autophosphorylation / membrane raft / protein-containing complex binding / innate immune response / protein phosphorylation / negative regulation of apoptotic process / ATP hydrolysis activity / protein-containing complex / mitochondrion / ATP binding / identical protein binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase, N-terminal / Hexokinase domain profile. / Hexokinase, binding site / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase / Hexokinase, C-terminal ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase, N-terminal / Hexokinase domain profile. / Hexokinase, binding site / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase / Hexokinase, C-terminal / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / 6-O-phosphono-alpha-D-glucopyranose / Hexokinase-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMulichak, A.M. / Garavito, R.M.
CitationJournal: Nat.Struct.Biol. / Year: 1998
Title: The structure of mammalian hexokinase-1.
Authors: Mulichak, A.M. / Wilson, J.E. / Padmanabhan, K. / Garavito, R.M.
History
DepositionJun 4, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEXOKINASE
B: HEXOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,89211
Polymers205,0902
Non-polymers1,8019
Water4,216234
1
A: HEXOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4666
Polymers102,5451
Non-polymers9215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEXOKINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4265
Polymers102,5451
Non-polymers8814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.100, 77.100, 137.100
Angle α, β, γ (deg.)90.00, 96.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999992, 0.001479, -0.003776), (-0.00247, -0.960616, 0.27787), (-0.003216, 0.277877, 0.96061)
Vector: 2.4096, -45.7803, 6.5478)
DetailsALTHOUGH ENZYME IS ACTIVE AS A MONOMER, DIMERIZATION OCCURS AT HIGH PROTEIN CONCENTRATION, PARTICULARLY IN THE PRESENCE OF THE INHIBITOR G6P

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Components

#1: Protein HEXOKINASE / / ATP-D-HEXOSE-6-PHOSPHOTRANSFERASE


Mass: 102545.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: BOTH MONOMERS HAVE TWO SMALL BREAKS AT KNOWN OR LIKELY TRYPSIN CLEAVAGE SITES. ALTHOUGH ENZYME IS ACTIVE AS A MONOMER, DIMERIZATION OCCURS AT HIGH PROTEIN CONCENTRATION, PARTICULARLY IN THE ...Details: BOTH MONOMERS HAVE TWO SMALL BREAKS AT KNOWN OR LIKELY TRYPSIN CLEAVAGE SITES. ALTHOUGH ENZYME IS ACTIVE AS A MONOMER, DIMERIZATION OCCURS AT HIGH PROTEIN CONCENTRATION, PARTICULARLY IN THE PRESENCE OF THE INHIBITOR G6P
Source: (natural) Rattus norvegicus (Norway rat) / Organ: BRAIN / Tissue: BRAIN / References: UniProt: P05708, hexokinase
#2: Sugar
ChemComp-BGC / beta-D-glucopyranose / Glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBOTH MONOMERS HAVE TWO SMALL BREAKS AT KNOWN OR LIKELY TRYPSIN CLEAVAGE SITES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 55 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %PEG40001reservoir
20.13 M1reservoirCaCl2
3100 mMimidazole1reservoir

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Data collection

DiffractionMean temperature: 153 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MSC FOCUSSING MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 54454 / % possible obs: 79 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 8
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3 / % possible all: 59
Reflection shell
*PLUS
% possible obs: 59 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HEXOKINASE FROM SCHISTOSOMA MANSONI

Resolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2404 5 %RANDOM
Rwork0.196 ---
obs0.196 46567 71 %-
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 27 104 3483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.77
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.32
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.9 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.31 180 2.2 %
Rwork0.269 1227 -
obs--37 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.32

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