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- PDB-9dn3: Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinas... -

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Basic information

Entry
Database: PDB / ID: 9dn3
TitleCrystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in Complex with an Inhibitor 9-cylcopentyladenine
ComponentsInositol-tetrakisphosphate 1-kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / inhibitor development / inositol phosphate kinase / inhibitor complex / cancer therapy / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development ...inositol-3,4,6-trisphosphate 1-kinase activity / inositol-tetrakisphosphate 1-kinase / inositol-1,3,4-trisphosphate 5/6-kinase / inositol-3,4,5,6-tetrakisphosphate 1-kinase activity / inositol-1,3,4-trisphosphate 6-kinase activity / inositol-1,3,4-trisphosphate 5-kinase activity / inositol-1,3,4,5-tetrakisphosphate 6-kinase activity / inositol trisphosphate metabolic process / Synthesis of pyrophosphates in the cytosol / neural tube development / Synthesis of IP3 and IP4 in the cytosol / necroptotic process / catalytic activity / isomerase activity / blood coagulation / Factors involved in megakaryocyte development and platelet production / hydrolase activity / apical plasma membrane / magnesium ion binding / signal transduction / ATP binding / cytosol
Similarity search - Function
Inositol-tetrakisphosphate 1-kinase, N-terminal / Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain / Inositol-tetrakisphosphate 1-kinase / Inositol 1,3,4-trisphosphate 5/6-kinase, ATP-grasp domain / Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
: / Inositol-tetrakisphosphate 1-kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWang, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIAES103340 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Biochemical and biophysical characterization of inositol-tetrakisphosphate 1-kinase inhibitors.
Authors: Ng, M.Y. / Wang, H. / Zhang, H. / Prucker, I. / Perera, L. / Goncharova, E. / Wamiru, A. / Jessen, H.J. / Stanley, R.E. / Shears, S.B. / Luo, J. / O'Keefe, B.R. / Wilson, B.A.P.
History
DepositionSep 16, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol-tetrakisphosphate 1-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6043
Polymers37,3041
Non-polymers2992
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.592, 60.244, 115.467
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Inositol-tetrakisphosphate 1-kinase / Inositol 1 / 3 / 4-trisphosphate 5/6-kinase / Inositol-triphosphate 5/6-kinase / Ins(1 / 4)P(3) 5/6-kinase


Mass: 37304.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13572, inositol-tetrakisphosphate 1-kinase, inositol-1,3,4-trisphosphate 5/6-kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-A1A7Y / 9-cyclopentyl-9H-purin-6-amine


Mass: 203.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H13N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: Hanging drops comprised 2 ul of 14 mg/mL protein solution and 2 ul of well buffer (21% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, and 10% Glycerol) that was present in the ...Details: Hanging drops comprised 2 ul of 14 mg/mL protein solution and 2 ul of well buffer (21% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, and 10% Glycerol) that was present in the reservoir. Crystal complexes with inhibitors were formed in a soaking buffer (25% (w/v) PEG 8000, 0.17 mM (NH4)2SO4, 85 mM Tris-HCl, pH 8.0, 20% Glycerol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920072 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920072 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 19525 / % possible obs: 99.7 % / Redundancy: 10.1 % / CC1/2: 0.951 / CC star: 0.998 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.034 / Rrim(I) all: 0.108 / Χ2: 1.088 / Net I/σ(I): 19.3
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 962 / CC1/2: 0.826 / CC star: 0.998 / Rpim(I) all: 0.245 / Rrim(I) all: 0.816 / Χ2: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874: ???refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→33.09 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2709 917 6.69 %RANDOM
Rwork0.2194 ---
obs0.2229 13706 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2529 0 20 62 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042598
X-RAY DIFFRACTIONf_angle_d0.7213518
X-RAY DIFFRACTIONf_dihedral_angle_d22.276357
X-RAY DIFFRACTIONf_chiral_restr0.05399
X-RAY DIFFRACTIONf_plane_restr0.006457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.370.35911280.27341777X-RAY DIFFRACTION100
2.37-2.520.36871290.26741797X-RAY DIFFRACTION100
2.52-2.710.34091280.26191792X-RAY DIFFRACTION100
2.71-2.980.29741300.2491813X-RAY DIFFRACTION100
2.98-3.420.29171300.23041824X-RAY DIFFRACTION100
3.42-4.30.28211330.19651845X-RAY DIFFRACTION100
4.3-33.090.21411390.20181941X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.023 Å / Origin y: -3.5159 Å / Origin z: -7.6426 Å
111213212223313233
T0.246 Å20.0185 Å2-0.0135 Å2-0.2225 Å20.0171 Å2--0.2978 Å2
L0.9366 °20.2013 °20.2102 °2-1.2406 °20.9243 °2--2.8335 °2
S0.0111 Å °-0.0292 Å °0.0553 Å °0.0933 Å °-0.0468 Å °0.0522 Å °-0.0223 Å °-0.0763 Å °0.0339 Å °
Refinement TLS groupSelection details: all

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