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- PDB-7n7o: Crystal Structure of PI5P4KIIAlpha complex with Palbociclib -

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Basic information

Entry
Database: PDB / ID: 7n7o
TitleCrystal Structure of PI5P4KIIAlpha complex with Palbociclib
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 / PI5P Regulates TP53 Acetylation ...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 / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / photoreceptor outer segment / autophagosome / negative regulation of insulin receptor signaling pathway / photoreceptor inner segment / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / phosphorylation / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Chem-LQQ / Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)43,7544
Polymers43,1151
Non-polymers6403
Water1,27971
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)87,5098
Polymers86,2292
Non-polymers1,2796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_527x,x-y-3,-z+13/61
Buried area4760 Å2
ΔGint-53 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.901, 135.901, 95.014
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-LQQ / 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE / Palbociclib / Palbociclib


Mass: 447.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29N7O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.94 Å3/Da / Density % sol: 58.13 %
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: 2.7→40 Å / Num. obs: 14739 / % possible obs: 100 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.02 / Rrim(I) all: 0.077 / Χ2: 0.995 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.814.70.84214360.9090.2270.8720.994100
2.8-2.9114.70.64514420.9420.1740.6680.992100
2.91-3.0414.70.38814270.980.1040.4020.994100
3.04-3.214.70.25314510.9970.0680.2620.997100
3.2-3.414.60.16814490.9960.0450.1740.97100
3.4-3.6614.50.11514570.9980.0310.1190.993100
3.66-4.0314.40.07714700.9990.0210.080.977100
4.03-4.6214.30.05914830.9990.0160.0610.99100
4.62-5.8114.20.05215020.9990.0140.0541.091100
5.81-4013.20.028162210.0080.030.94799.9

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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: 2.7→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / SU B: 10.098 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.424 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 700 4.8 %RANDOM
Rwork0.1969 ---
obs0.1997 14011 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.76 Å2 / Biso mean: 72.483 Å2 / Biso min: 37.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å20 Å2
2--1.46 Å2-0 Å2
3----4.73 Å2
Refinement stepCycle: final / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 43 71 2491
Biso mean--94.36 68.09 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192477
X-RAY DIFFRACTIONr_angle_refined_deg1.2431.9683365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8625298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44924.174115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34515391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8561511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211887
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 45 -
Rwork0.259 1020 -
all-1065 -
obs--100 %

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