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- PDB-6m8e: Crystal structure of the core catalytic domain of human inositol ... -

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Basic information

Entry
Database: PDB / ID: 6m8e
TitleCrystal structure of the core catalytic domain of human inositol phosphate multikinase in complex with rhamnetin
ComponentsInositol polyphosphate multikinase,Inositol polyphosphate multikinase
KeywordsTRANSFERASE/TRANSFERASE Inhibitor / kinase / inositol / inositol polyphosphate / TRANSFERASE / rhamnetin / 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-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol-1,3,4,6-tetrakisphosphate 5-kinase activity / flavonoid binding / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity ...inositol tetrakisphosphate kinase activity / Synthesis of IPs in the nucleus / inositol-tetrakisphosphate 5-kinase / inositol-1,2,3,4,6-pentakisphosphate 5-kinase activity / inositol-polyphosphate multikinase / inositol-1,4,5-trisphosphate 6-kinase activity / inositol-1,4,5,6-tetrakisphosphate 3-kinase activity / inositol-1,3,4,6-tetrakisphosphate 5-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-J8G / 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)30,1442
Polymers29,8281
Non-polymers3161
Water1,946108
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)78.152, 78.152, 85.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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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-J8G / 2-(3,4-dihydroxyphenyl)-3,5-dihydroxy-7-methoxy-4H-1-benzopyran-4-one / rhamnetin


Mass: 316.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C16H12O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
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 rhametine for 3 days.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 19, 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: 18331 / % possible obs: 99.5 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.02 / Rrim(I) all: 0.077 / Χ2: 1.011 / Net I/σ(I): 29.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 882 / CC1/2: 0.901 / Rpim(I) all: 0.222 / Rrim(I) all: 0.833 / Χ2: 0.78 / % 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→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.92 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24508 943 5.2 %RANDOM
Rwork0.18431 ---
obs0.18729 17229 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.315 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å2-0 Å2-0 Å2
2--1.17 Å2-0 Å2
3----2.34 Å2
Refinement stepCycle: 1 / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 23 108 2072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192162
X-RAY DIFFRACTIONr_bond_other_d0.0010.021938
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.9772955
X-RAY DIFFRACTIONr_angle_other_deg0.8813.0014530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2825270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57724.158101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68415373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212478
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
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_it1.9172.8991035
X-RAY DIFFRACTIONr_mcbond_other1.9122.8971034
X-RAY DIFFRACTIONr_mcangle_it2.6054.3291320
X-RAY DIFFRACTIONr_mcangle_other2.6064.331321
X-RAY DIFFRACTIONr_scbond_it1.9453.2521127
X-RAY DIFFRACTIONr_scbond_other1.9323.2481121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5834.7851630
X-RAY DIFFRACTIONr_long_range_B_refined4.11134.2912501
X-RAY DIFFRACTIONr_long_range_B_other4.10834.2752497
X-RAY DIFFRACTIONr_rigid_bond_restr0.7234099
X-RAY DIFFRACTIONr_sphericity_free44.322541
X-RAY DIFFRACTIONr_sphericity_bonded24.10954096
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 54 -
Rwork0.205 1137 -
obs--89.55 %

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