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- PDB-7n7j: Crystal Structure of PI5P4KIIAlpha complex with AMPPNP -

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Basic information

Entry
Database: PDB / ID: 7n7j
TitleCrystal Structure of PI5P4KIIAlpha complex with AMPPNP
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 / negative regulation of insulin receptor signaling pathway / autophagosome / photoreceptor inner segment / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / lysosome / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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)44,0197
Polymers43,1151
Non-polymers9046
Water3,279182
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)88,03814
Polymers86,2292
Non-polymers1,80912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_527x,x-y-3,-z+13/61
Buried area5590 Å2
ΔGint-125 kcal/mol
Surface area28950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.074, 136.074, 95.141
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 182 / 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: 58.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Lithium sulfate monohydate, 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: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 30655 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Χ2: 1.088 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1813.10.71129960.8670.2010.741.03599.7
2.18-2.2613.10.53430050.9050.1510.5551.10999.9
2.26-2.3713.10.38530150.9590.1090.4010.94299.9
2.37-2.4913.30.25830220.9830.0730.2680.94199.9
2.49-2.6513.50.19430380.990.0540.2021.08999.9
2.65-2.8513.80.13630410.9950.0370.1411.12899.9
2.85-3.1414.20.09630590.9970.0260.0991.04100
3.14-3.5914.30.07430940.9980.020.0761.169100
3.59-4.52140.05731320.9990.0160.0591.163100
4.52-4013.20.03832530.9990.0110.0391.2498.1

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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: 2.1→40 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.706 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 1455 4.7 %RANDOM
Rwork0.2129 ---
obs0.2147 29179 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 124.39 Å2 / Biso mean: 49.138 Å2 / Biso min: 23.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: final / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 48 182 2698
Biso mean--66.57 50.15 -
Num. residues----313
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192569
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9713485
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6795309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09524.103117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67915421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9261511
X-RAY DIFFRACTIONr_chiral_restr0.0760.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211921
LS refinement shellResolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 103 -
Rwork0.334 2115 -
all-2218 -
obs--99.55 %

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