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- PDB-7n7n: Crystal Structure of PI5P4KIIAlpha complex with Volasertib -

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Basic information

Entry
Database: PDB / ID: 7n7n
TitleCrystal Structure of PI5P4KIIAlpha complex with Volasertib
ComponentsPhosphatidylinositol 5-phosphate 4-kinase type-2 alpha
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


vesicle-mediated cholesterol transport / 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / megakaryocyte development / phosphatidylinositol phosphate biosynthetic process ...vesicle-mediated cholesterol transport / 1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / megakaryocyte development / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / photoreceptor outer segment / photoreceptor inner segment / negative regulation of insulin receptor signaling pathway / autophagosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / regulation of autophagy / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol-4-phosphate 5-kinase / Phosphatidylinositol-4-phosphate 5-kinase, core / : / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-IBI / Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChen, S. / Ha, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Pharmacological inhibition of PI5P4K alpha / beta disrupts cell energy metabolism and selectively kills p53-null tumor cells.
Authors: Chen, S. / Chandra Tjin, C. / Gao, X. / Xue, Y. / Jiao, H. / Zhang, R. / Wu, M. / He, Z. / Ellman, J. / Ha, Y.
History
DepositionJun 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / Item: _citation.journal_abbrev / _citation.title
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0225
Polymers43,1151
Non-polymers9074
Water2,162120
1
A: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
hetero molecules

A: Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,04310
Polymers86,2292
Non-polymers1,8148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_527x,x-y-3,-z+13/61
Buried area3360 Å2
ΔGint-85 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.070, 136.070, 95.185
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha / 1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha / Diphosphoinositide kinase 2-alpha / PIP5KIII ...1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha / Diphosphoinositide kinase 2-alpha / PIP5KIII / Phosphatidylinositol 5-Phosphate 4-Kinase / PI5P4Kalpha / Phosphatidylinositol 5-phosphate 4-kinase type II alpha / PI(5)P 4-kinase type II alpha / PIP4KII-alpha / PtdIns(4)P-5-kinase B isoform / PtdIns(4)P-5-kinase C isoform / PtdIns(5)P-4-kinase isoform 2-alpha


Mass: 43114.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2A, PI5P4KA, PIP5K2, PIP5K2A / Production host: Escherichia coli (E. coli)
References: UniProt: P48426, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Chemical ChemComp-IBI / N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide / Volasertib


Mass: 618.813 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H50N8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 23633 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.021 / Rrim(I) all: 0.08 / Χ2: 1.001 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.3814.10.57723290.9470.1570.5980.99100
2.38-2.4814.10.4422930.9690.120.4560.973100
2.48-2.5914.20.32923240.9820.0890.3410.907100
2.59-2.7313.90.30223240.9690.0840.3141.2100
2.73-2.914.50.16823190.9920.0450.1740.979100
2.9-3.1214.60.12423450.9950.0330.1280.975100
3.12-3.4414.50.09623530.9980.0260.0990.936100
3.44-3.9314.10.08223730.9970.0230.0851.062100
3.93-4.9514.30.06424120.9980.0170.0661.048100
4.95-4013.40.04525610.9990.0130.0470.9599.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0218refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
REFMAC5.8.0218phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YBX

2ybx


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.984 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 1174 5 %RANDOM
Rwork0.2144 ---
obs0.2165 22411 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 182.7 Å2 / Biso mean: 60.603 Å2 / Biso min: 31.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.38 Å20 Å2
2--0.77 Å20 Å2
3----2.49 Å2
Refinement stepCycle: final / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 60 120 2559
Biso mean--117.67 59.25 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0192495
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9753388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89124.018112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.04715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9731511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211877
LS refinement shellResolution: 2.3→2.359 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.298 83 -
Rwork0.277 1617 -
obs--99.3 %

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