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- PDB-7qpn: Crystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (P... -

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Basic information

Entry
Database: PDB / ID: 7qpn
TitleCrystal Structure of Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C) bound to an allosteric inhibitor and AMP-PNP
ComponentsPhosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C)
KeywordsTRANSFERASE / ALLOSTERIC BINDING / LIPID KINASE / NON-ATP-COMPETITIVE INHIBITOR / phosphatidylinositol 5-phosphate
Function / homologyPhosphatidylinositol Phosphate Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / 2-Layer Sandwich / Alpha Beta / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Chem-DVF
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHoward, T.D. / Ogg, D.T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Alzheimers Research UK (ARUK)ARUK-2015DDI-CAM United Kingdom
CitationJournal: J.Med.Chem. / Year: 2022
Title: Development of Selective Phosphatidylinositol 5-Phosphate 4-Kinase gamma Inhibitors with a Non-ATP-competitive, Allosteric Binding Mode.
Authors: Boffey, H.K. / Rooney, T.P.C. / Willems, H.M.G. / Edwards, S. / Green, C. / Howard, T. / Ogg, D. / Romero, T. / Scott, D.E. / Winpenny, D. / Duce, J. / Skidmore, J. / Clarke, J.H. / Andrews, S.P.
History
DepositionJan 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 17, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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 (PI5P4K2C)
B: Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0256
Polymers80,2982
Non-polymers1,7274
Water3,783210
1
A: Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0133
Polymers40,1491
Non-polymers8642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0133
Polymers40,1491
Non-polymers8642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.921, 65.625, 117.120
Angle α, β, γ (deg.)90.000, 93.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphatidylinositol 5-Phosphate 4-Kinase (PI5P4K2C)


Mass: 40148.898 Da / Num. of mol.: 2 / Mutation: aa32-421(delta 300-341)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
#2: Chemical ChemComp-DVF / 5-methyl-2-(2-propan-2-ylphenyl)-~{N}-(pyridin-2-ylmethyl)pyrrolo[3,2-d]pyrimidin-4-amine


Mass: 357.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23N5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% Peg5KMME, 0.3M Ammonium Tartrate, 100mM PCTP, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.95→116.94 Å / Num. obs: 39543 / % possible obs: 91.7 % / Redundancy: 5.4 % / CC1/2: 0.996 / Net I/σ(I): 9.2
Reflection shellResolution: 1.95→2.14 Å / Redundancy: 5.1 % / Num. unique obs: 1978 / CC1/2: 0.56 / % possible all: 56.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GK9

2gk9


Resolution: 1.95→116.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.015 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1877 4.7 %RANDOM
Rwork0.1919 ---
obs0.1951 37666 74.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.25 Å2 / Biso mean: 47.45 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0.01 Å2
2---0.54 Å2-0 Å2
3---1.22 Å2
Refinement stepCycle: final / Resolution: 1.95→116.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5133 0 143 210 5486
Biso mean--63.61 46.26 -
Num. residues----630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0135406
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165077
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6447308
X-RAY DIFFRACTIONr_angle_other_deg1.2271.60311689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.60222.305295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71815945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3891534
X-RAY DIFFRACTIONr_chiral_restr0.070.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026349
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021261
LS refinement shellResolution: 1.95→1.997 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rwork0.319 33 -
obs--84 %

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