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- PDB-6m8d: Crystal structure of the core catalytic domain of human inositol ... -

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Basic information

Entry
Database: PDB / ID: 6m8d
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with diosmetin
ComponentsInositol polyphosphate multikinase,Inositol polyphosphate multikinase
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / kinase / inositol / inositol polyphosphate / TRANSFERASE / diosmetin / flavonoid / inhibitor / natural product / TRANSFERASE-TRANSFERASE Inhibitor complex
Function / homology
Function and homology information


inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity ...inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol trisphosphate metabolic process / inositol phosphate metabolic process / inositol phosphate biosynthetic process / phosphatidylinositol metabolic process / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / phosphatidylinositol-4,5-bisphosphate 3-kinase / necroptotic process / ciliary basal body / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
Chem-J8D / Inositol polyphosphate multikinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsWang, H. / Shears, S.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES080046-29 United States
CitationJournal: J. Med. Chem. / Year: 2019
Title: Inhibition of Inositol Polyphosphate Kinases by Quercetin and Related Flavonoids: A Structure-Activity Analysis.
Authors: Gu, C. / Stashko, M.A. / Puhl-Rubio, A.C. / Chakraborty, M. / Chakraborty, A. / Frye, S.V. / Pearce, K.H. / Wang, X. / Shears, S.B. / Wang, H.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Inositol polyphosphate multikinase,Inositol polyphosphate multikinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1282
Polymers29,8281
Non-polymers3001
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.971, 77.971, 85.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

21A-721-

HOH

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Components

#1: Protein Inositol polyphosphate multikinase,Inositol polyphosphate multikinase / Inositol 1 / 3 / 4 / 6-tetrakisphosphate 5-kinase


Mass: 29827.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IPMK, IMPK / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NFU5, inositol-polyphosphate multikinase
#2: Chemical ChemComp-J8D / 5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-4H-1-benzopyran-4-one / diosmetin


Mass: 300.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H12O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 43.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG ...Details: 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM MES Imidanzol buffer , pH 6.0, 50 mM beta-mercaptoethanol at 298K. To obtain complex structure, the apo crystal was further soaked under 35% (w/v) PEG 400, 0.1 M Li2SO4, 100 mM HEPES, pH 7.5 at 298K in the presence of 10 mM diosmetin for 3 days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18315 / % possible obs: 99.5 % / Redundancy: 7.8 % / Biso Wilson estimate: 22.79 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.032 / Rrim(I) all: 0.096 / Χ2: 1.064 / Net I/σ(I): 22.3
Reflection shellResolution: 2→2.03 Å / Redundancy: 8 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 877 / CC1/2: 0.786 / Rpim(I) all: 0.317 / Rrim(I) all: 0.955 / Χ2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5w2g

5w2g


Resolution: 2→38 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.811 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R Free: 0.173 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23949 947 5.2 %RANDOM
Rwork0.17314 ---
obs0.17644 17172 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0 Å2-0 Å2
2--0.31 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 2→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 22 134 2097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192051
X-RAY DIFFRACTIONr_bond_other_d0.0020.021848
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.9752784
X-RAY DIFFRACTIONr_angle_other_deg0.8793.0014310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4695246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64924.22797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.715351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.013159
X-RAY DIFFRACTIONr_chiral_restr0.0650.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212286
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02427
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_it1.8482.966975
X-RAY DIFFRACTIONr_mcbond_other1.8512.964974
X-RAY DIFFRACTIONr_mcangle_it2.7494.4381224
X-RAY DIFFRACTIONr_mcangle_other2.7524.4391225
X-RAY DIFFRACTIONr_scbond_it1.9423.2021075
X-RAY DIFFRACTIONr_scbond_other1.9413.2011076
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5414.7431560
X-RAY DIFFRACTIONr_long_range_B_refined4.535.2742381
X-RAY DIFFRACTIONr_long_range_B_other4.24135.0382361
X-RAY DIFFRACTIONr_rigid_bond_restr0.69433894
X-RAY DIFFRACTIONr_sphericity_free46.746570
X-RAY DIFFRACTIONr_sphericity_bonded27.04653908
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 60 -
Rwork0.203 1139 -
obs--90.9 %

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