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- PDB-1qha: HUMAN HEXOKINASE TYPE I COMPLEXED WITH ATP ANALOGUE AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 1qha
TitleHUMAN HEXOKINASE TYPE I COMPLEXED WITH ATP ANALOGUE AMP-PNP
ComponentsPROTEIN (HEXOKINASE)
KeywordsTRANSFERASE / KINASE / GLYCOLYSIS / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / hexokinase activity / mannokinase activity / maintenance of protein location in mitochondrion / positive regulation of cytokine production involved in immune response / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation ...Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / hexokinase activity / mannokinase activity / maintenance of protein location in mitochondrion / positive regulation of cytokine production involved in immune response / establishment of protein localization to mitochondrion / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / peptidoglycan binding / glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / positive regulation of interleukin-1 beta production / glycolytic process / glucose metabolic process / mitochondrial outer membrane / inflammatory response / membrane raft / innate immune response / mitochondrion / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 6-O-phosphono-alpha-D-glucopyranose / alpha-D-glucopyranose / Hexokinase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsRosano, C. / Sabini, E. / Deriu, D. / Magnani, M. / Bolognesi, M.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: Binding of non-catalytic ATP to human hexokinase I highlights the structural components for enzyme-membrane association control.
Authors: Rosano, C. / Sabini, E. / Rizzi, M. / Deriu, D. / Murshudov, G. / Bianchi, M. / Serafini, G. / Magnani, M. / Bolognesi, M.
#1: Journal: Protein Pept.Lett. / Year: 1998
Title: Expression, Purification and Preliminary Crystallographic Studies of Human Hexokinase I
Authors: Sabini, E. / Rosano, C. / Capasso, C. / Rizzi, M. / Bolognesi, M. / Bianchi, M. / Serafini, G. / Bartolucci, E. / Magnani, M.
History
DepositionMay 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Nov 10, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HEXOKINASE)
B: PROTEIN (HEXOKINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,16818
Polymers205,2482
Non-polymers2,91916
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.590, 176.170, 86.760
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PROTEIN (HEXOKINASE)


Mass: 102624.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ATP ANALOGUE AMP-PNP / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19367, hexokinase

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Sugars , 2 types, 8 molecules

#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: isolated from a natural 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-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


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

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Non-polymers , 3 types, 468 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details4 MOLECULES IN ALPHA-ANOMER CONFORMATION ATP NON-HYDROLYZABLE ANALOGUE

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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: 3.11 Å3/Da / Density % sol: 60.47 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop
Details: drop contained 0.004ml solutionA, 0.001ml reservoir solution and 0.001ml solutionB.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 %(w/v)PEG80001reservoir
2200 mMmagnesium acetate1reservoir
3100 mMsodium acetate1reservoir
410 %(v/v)glycerol1reservoir
53 mMbeta-mercaptoethanol1reservoir
615 mg/mlprotein1dropsolutionA
710 mMglucose1dropsolutionA
83 mMbeta-mercaptoethanol1dropsolutionA
99 %(v/v)glycerol1dropsolutionA
1040 mM1dropsolutionAKCl
111.5 mMG6P1dropsolutionA
1260 mMAMP-PNP1dropsolutionB

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.936
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.936 Å / Relative weight: 1
ReflectionResolution: 2.25→38 Å / Num. obs: 102729 / % possible obs: 86.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Rsym value: 0.097 / Net I/σ(I): 8
Reflection shellResolution: 2.25→2.3 Å / Mean I/σ(I) obs: 6.8
Reflection
*PLUS
Num. measured all: 405442 / Rmerge(I) obs: 0.05

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HKB

1hkb


Resolution: 2.25→12 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.279 5081 5 %RANDOM
Rwork0.208 ---
obs-96872 85 %-
Refinement stepCycle: LAST / Resolution: 2.25→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14097 0 180 460 14737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.039
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 12 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS

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