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- PDB-3hm8: Crystal structure of the C-terminal Hexokinase domain of human HK3 -

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Basic information

Entry
Database: PDB / ID: 3hm8
TitleCrystal structure of the C-terminal Hexokinase domain of human HK3
ComponentsHexokinase-3
KeywordsTRANSFERASE / glucose / glucose-6-phosphate / non-protein kinase / hexokinase / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / Allosteric enzyme / ATP-binding / Glycolysis / Kinase / Nucleotide-binding
Function / homology
Function and homology information


hexokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis ...hexokinase activity / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / D-glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / mitochondrion / extracellular region / ATP binding / cytosol
Similarity search - Function
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. ...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 / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / alpha-D-glucopyranose / Hexokinase-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.8 Å
AuthorsNedyalkova, L. / Tong, Y. / Rabeh, W. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Nedyalkova, L. / Tong, Y. / Rabeh, W. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the C-terminal Hexokinase domain of human HK3
Authors: Nedyalkova, L. / Tong, Y. / Rabeh, W. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / 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_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hexokinase-3
B: Hexokinase-3
C: Hexokinase-3
D: Hexokinase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,23512
Polymers193,4744
Non-polymers1,7618
Water00
1
A: Hexokinase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8093
Polymers48,3681
Non-polymers4402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hexokinase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8093
Polymers48,3681
Non-polymers4402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hexokinase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8093
Polymers48,3681
Non-polymers4402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hexokinase-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8093
Polymers48,3681
Non-polymers4402
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.904, 83.904, 323.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D
15A
25B
35C
45D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A479 - 773
2111B479 - 773
3111C479 - 773
4111D479 - 773
1124A774 - 778
2124B774 - 778
3124C774 - 778
4124D774 - 778
1131A779 - 799
2131B779 - 799
3131C779 - 799
4131D779 - 799
1144A800 - 826
2144B800 - 826
3144C800 - 826
4144D800 - 826
1151A827 - 1002
2151B827 - 1002
3151C827 - 1002
4151D827 - 1002

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Hexokinase-3 / Hexokinase type III / HK III


Mass: 48368.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK3 / Plasmid: pET28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P52790, hexokinase
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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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 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 291 K / pH: 7.2
Details: reservoir solution: 16% PEG 3350, 0.20 M Ammonium Citrate, 0.1 M HEPES. 0.005 M glucose-6-phosphate, 0.005 M ADP-Mg, 0.02 M TCEP, 1:100 (w/w) trypsin was added to the protein stock solution. ...Details: reservoir solution: 16% PEG 3350, 0.20 M Ammonium Citrate, 0.1 M HEPES. 0.005 M glucose-6-phosphate, 0.005 M ADP-Mg, 0.02 M TCEP, 1:100 (w/w) trypsin was added to the protein stock solution., pH 7.2, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 53686 / % possible obs: 98.4 %
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.666 / % possible all: 86.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: molecular replacement
Starting model: pdb entry 2NZT, chain A, residues 468 through 913

2nzt


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 48.382 / SU ML: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROGRAMS CHAINSAW, PRODRG, PHENIX, COOT AND MOLPROBLITY WERE ALSO USED.
RfactorNum. reflection% reflection
Rfree0.27 1502 2.837 %
Rwork0.245 --
obs0.245 52939 97.2 %
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.541 Å20 Å20 Å2
2--5.541 Å20 Å2
3----11.082 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12521 0 112 0 12633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02212803
X-RAY DIFFRACTIONr_bond_other_d0.0030.028173
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9817404
X-RAY DIFFRACTIONr_angle_other_deg0.7833.00119913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.86451749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61224.103468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.488151929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3041578
X-RAY DIFFRACTIONr_chiral_restr0.0590.22118
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0214625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022533
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.071.58655
X-RAY DIFFRACTIONr_mcbond_other0.031.53620
X-RAY DIFFRACTIONr_mcangle_it0.137213638
X-RAY DIFFRACTIONr_scbond_it0.34234148
X-RAY DIFFRACTIONr_scangle_it0.5764.53766
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3356tight positional0.020.05
12B3356tight positional0.010.05
13C3356tight positional0.010.05
14D3356tight positional0.010.05
31A233tight positional0.030.05
32B233tight positional0.020.05
33C233tight positional0.010.05
34D233tight positional0.010.05
51A1041tight positional0.020.05
52B1041tight positional0.010.05
53C1041tight positional0.020.05
54D1041tight positional0.010.05
21A20medium positional0.130.5
22B20medium positional0.230.5
23C20medium positional0.220.5
24D20medium positional0.10.5
41A261medium positional0.190.5
42B261medium positional0.390.5
43C261medium positional0.280.5
44D261medium positional0.290.5
11A3356tight thermal0.020.5
12B3356tight thermal0.020.5
13C3356tight thermal0.020.5
14D3356tight thermal0.020.5
31A233tight thermal0.030.5
32B233tight thermal0.030.5
33C233tight thermal0.020.5
34D233tight thermal0.030.5
51A1041tight thermal0.030.5
52B1041tight thermal0.020.5
53C1041tight thermal0.020.5
54D1041tight thermal0.020.5
21A20medium thermal0.172
22B20medium thermal0.092
23C20medium thermal0.132
24D20medium thermal0.122
41A261medium thermal0.182
42B261medium thermal0.192
43C261medium thermal0.122
44D261medium thermal0.122
LS refinement shellResolution: 2.8→2.87 Å
RfactorNum. reflection% reflection
Rwork0.406 3210 -
Rfree-0 -
obs--82.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5995-0.8355-0.93351.62921.08043.69540.2508-0.1380.03770.0117-0.1666-0.1735-0.39160.1009-0.08420.1513-0.05890.01620.06710.02760.180711.6237-0.8335-27.4201
23.24131.1504-0.33992.5303-1.31594.93150.07650.57380.0271-0.0847-0.0372-0.1213-0.42390.2217-0.03930.1795-0.07050.04390.2517-0.01910.330432.938843.940211.1335
32.79290.42731.68452.4697-0.03225.10490.3385-0.3091-0.2537-0.0035-0.17170.2850.1323-0.8575-0.16680.1596-0.17770.00860.3709-0.03860.1778-7.3558-3.13649.1463
42.8234-1.04851.33052.81080.06414.4730.1518-0.0705-0.08150.0439-0.0226-0.21270.12120.5534-0.12920.10110.19210.03550.52210.09380.378752.851140.0313-24.4231
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 1002
2X-RAY DIFFRACTION2B1 - 1002
3X-RAY DIFFRACTION3C1 - 1002
4X-RAY DIFFRACTION4D1 - 1002

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