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- PDB-2nzt: Crystal structure of human hexokinase II -

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Basic information

Entry
Database: PDB / ID: 2nzt
TitleCrystal structure of human hexokinase II
ComponentsHexokinase-2
KeywordsTRANSFERASE / glucose / glucose-6-phosphate / non-protein kinase / hexokinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / regulation of glucose import / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity ...negative regulation of mitochondrial membrane permeability / hexokinase activity / maintenance of protein location in mitochondrion / positive regulation of autophagy of mitochondrion in response to mitochondrial depolarization / regulation of glucose import / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / apoptotic mitochondrial changes / intracellular glucose homeostasis / negative regulation of reactive oxygen species metabolic process / lactation / cellular response to leukemia inhibitory factor / sarcoplasmic reticulum / response to ischemia / glycolytic process / glucose metabolic process / positive regulation of angiogenesis / mitochondrial outer membrane / response to hypoxia / intracellular membrane-bounded organelle / centrosome / mitochondrion / ATP binding / membrane / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsRabeh, W.M. / Zhu, H. / Nedyalkova, L. / Tempel, W. / Wasney, G. / Landry, R. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. ...Rabeh, W.M. / Zhu, H. / Nedyalkova, L. / Tempel, W. / Wasney, G. / Landry, R. / Vedadi, M. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: Biosci.Rep. / Year: 2018
Title: The catalytic inactivation of the N-half of human hexokinase 2 and structural and biochemical characterization of its mitochondrial conformation.
Authors: Nawaz, M.H. / Ferreira, J.C. / Nedyalkova, L. / Zhu, H. / Carrasco-Lopez, C. / Kirmizialtin, S. / Rabeh, W.M.
History
DepositionNov 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 15, 2020Group: Data collection / Database references
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_ref_seq_dif
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 30, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300SEQUENCE BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS ...SEQUENCE BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT OF THE PROTEIN IS NOT KNOWN

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hexokinase-2
B: Hexokinase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,99138
Polymers201,2302
Non-polymers1,76136
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-11 kcal/mol
Surface area64950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.890, 129.338, 187.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12A
22B
13A
23B
14B
24A

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHEBB197 - 199183 - 185
21GLYGLYPHEPHEAA197 - 199183 - 185
12ASPASPVALVALAA650 - 652636 - 638
22ASPASPVALVALBB650 - 652636 - 638
13ASPASPHISHISAA669 - 671655 - 657
23ASPASPHISHISBB669 - 671655 - 657
14ILEILEGLUGLUBB772 - 774758 - 760
24ILEILEGLUGLUAA772 - 774758 - 760

NCS ensembles :
ID
1
2
3
4
Detailsnot known

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Components

#1: Protein Hexokinase-2 / / Hexokinase type II / HK II / Muscle form hexokinase


Mass: 100614.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HK2 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL / References: UniProt: P52789, hexokinase
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 28 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1358
2358
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16% PEG3350, 0.2M sodium malonate, 0.1M BTP, 10% ethylene glycol, 0.001M DDT, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Aug 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 85698 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.082 / Χ2: 1.511 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2
2.45-2.541004.90.67184481.038
2.54-2.6499.950.55184791.118
2.64-2.7699.850.43384791.449
2.76-2.999.95.20.31184901.325
2.9-3.0999.95.30.22185361.542
3.09-3.3299.95.40.15385081.828
3.32-3.6699.95.60.10885681.787
3.66-4.1999.85.80.07886011.673
4.19-5.2799.86.40.05786601.459
5.27-3099.36.60.04389291.701

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
Cootmodel building
PRODRGrefinement
MolProbitymodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1cza

1cza


Resolution: 2.45→25 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.897 / WRfactor Rfree: 0.286 / WRfactor Rwork: 0.227 / SU B: 13.527 / SU ML: 0.291 / ESU R: 0.402 / ESU R Free: 0.291 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 2083 2.49 %thin shells
Rwork0.2301 ---
all0.232 ---
obs-83669 98.172 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.349 Å2
Baniso -1Baniso -2Baniso -3
1-1.448 Å20 Å20 Å2
2---2.777 Å20 Å2
3---1.329 Å2
Refinement stepCycle: LAST / Resolution: 2.45→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13309 0 140 97 13546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02213618
X-RAY DIFFRACTIONr_bond_other_d0.0030.029241
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.97718350
X-RAY DIFFRACTIONr_angle_other_deg1.3493.00122419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44751725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15523.854589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.766152426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.71415101
X-RAY DIFFRACTIONr_chiral_restr0.080.22125
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022720
X-RAY DIFFRACTIONr_nbd_refined0.2150.23090
X-RAY DIFFRACTIONr_nbd_other0.2040.29747
X-RAY DIFFRACTIONr_nbtor_refined0.1820.26686
X-RAY DIFFRACTIONr_nbtor_other0.0940.27619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2395
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.23
X-RAY DIFFRACTIONr_mcbond_it0.7131.58870
X-RAY DIFFRACTIONr_mcbond_other0.0721.53588
X-RAY DIFFRACTIONr_mcangle_it1.18213707
X-RAY DIFFRACTIONr_mcangle_other0.587211384
X-RAY DIFFRACTIONr_scbond_it1.49335343
X-RAY DIFFRACTIONr_scbond_other0.66537068
X-RAY DIFFRACTIONr_scangle_it2.3364.54643
X-RAY DIFFRACTIONr_scangle_other1.124.511035
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B17tight positional0.0290.05
2A18tight positional0.0420.05
3A17tight positional0.0390.05
4B18tight positional0.0580.05
1B22medium positional0.3320.5
2A14medium positional0.1870.5
3A25medium positional0.2710.5
4B18medium positional0.3930.5
1B17tight thermal0.0590.5
2A18tight thermal0.1280.5
3A17tight thermal0.0870.5
4B18tight thermal0.2540.5
1B22medium thermal0.3462
2A14medium thermal0.292
3A25medium thermal0.4482
4B18medium thermal0.3442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.45-2.51300.30761560.307618899.483
2.513-2.58100.31559880.315603799.188
2.581-2.65500.33157410.331582498.575
2.655-2.7360.3557990.31648290.321571298.529
2.736-2.82500.30854370.308553098.318
2.825-2.92200.31452370.314535997.723
2.922-3.03100.29550580.295518297.607
3.031-3.15300.28648940.286502497.412
3.153-3.2910.3215750.27340990.279479297.538
3.291-3.44800.25544620.255456597.744
3.448-3.63100.23742510.237440396.548
3.631-3.84600.21440280.214416096.827
3.846-4.1050.2583610.19234840.198393497.738
4.105-4.42400.17835750.178365897.731
4.424-4.83100.16433410.164339798.351
4.831-5.3760.2811750.18528850.19310898.456
5.376-6.1610.229410.22127140.221277799.208
6.161-7.43300.21723710.217238299.538
7.433-10.0760.21020.15918110.162192399.48
10.076-250.346300.2112250.213127298.664

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