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- PDB-8q6f: HUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 4) -

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Basic information

Entry
Database: PDB / ID: 8q6f
TitleHUMAN PI4KIIIB IN COMPLEX WITH COVALENTLY BOUND INHIBITOR (COMPOUND 4)
ComponentsPhosphatidylinositol 4-kinase beta
KeywordsTRANSFERASE / LIPID KINASE / TRANSFERASE-SIGNALING PROTEIN COMPLEX / COVALENT INHIBITOR.
Function / homology
Function and homology information


1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / lysosome organization / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding ...1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / rough endoplasmic reticulum membrane / Synthesis of PIPs at the Golgi membrane / phosphatidylinositol biosynthetic process / lysosome organization / phosphatidylinositol-mediated signaling / phosphatidylinositol phosphate biosynthetic process / inner ear development / 14-3-3 protein binding / receptor-mediated endocytosis / kinase activity / mitochondrial outer membrane / endosome / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / ATP binding / membrane / cytosol / cytoplasm
Similarity search - Function
: / PI4KB/PIK1, accessory (PIK) domain / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain ...: / PI4KB/PIK1, accessory (PIK) domain / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-KHR / Phosphatidylinositol 4-kinase beta / Phosphatidylinositol 4-kinase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.506 Å
AuthorsSomers, D.O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Rsc Chem Biol / Year: 2023
Title: Covalent targeting of non-cysteine residues in PI4KIII beta.
Authors: Cosgrove, B. / Grant, E.K. / Bertrand, S. / Down, K.D. / Somers, D.O. / P Evans, J. / Tomkinson, N.C.O. / Barker, M.D.
History
DepositionAug 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 4-kinase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,41211
Polymers48,4041
Non-polymers1,00810
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint18 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.211, 67.553, 106.932
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphatidylinositol 4-kinase beta / PI4K-beta / PI4Kbeta / PtdIns 4-kinase beta / NPIK / PI4K92 / PI4KIII


Mass: 48403.625 Da / Num. of mol.: 1 / Mutation: R409Q,R412Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4KB, PIK4CB, PI4KB / Production host: Baculovirus expression vector pFastBac1-HM
References: UniProt: Q9UBF8, UniProt: A0A0B4J1S8, 1-phosphatidylinositol 4-kinase

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Non-polymers , 5 types, 354 molecules

#2: Chemical ChemComp-KHR / 3-(3-fluorosulfonyloxy-4-methoxy-phenyl)-2,5-dimethyl-7-(pyridin-4-ylmethylamino)pyrazolo[1,5-a]pyrimidine


Mass: 457.478 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20FN5O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Sodium Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.506→57.111 Å / Num. obs: 43748 / % possible obs: 87.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Net I/σ(I): 16.5
Reflection shellResolution: 1.506→1.62 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.647 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2187 / CC1/2: 0.766 / Rpim(I) all: 0.381 / Rrim(I) all: 0.754 / % possible all: 64.5

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Processing

Software
NameVersionClassification
autoPROCv1.1.7data processing
XDSVERSION Jan 10, 2022data reduction
Aimlessv0.7.9data scaling
STARANISOv2.3.92data scaling
REFMAC5.8.0405phasing
REFMAC5.8.0405refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.506→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.017 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22386 2188 5 %RANDOM
Rwork0.17923 ---
obs0.18147 41521 63.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.475 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.506→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 66 344 3534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123361
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163254
X-RAY DIFFRACTIONr_angle_refined_deg1.1071.6494551
X-RAY DIFFRACTIONr_angle_other_deg0.3791.5767497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.655413
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.601521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1610609
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0560.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02773
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9636.4851620
X-RAY DIFFRACTIONr_mcbond_other3.9616.4851621
X-RAY DIFFRACTIONr_mcangle_it5.30912.4032043
X-RAY DIFFRACTIONr_mcangle_other5.30912.4022044
X-RAY DIFFRACTIONr_scbond_it5.3717.6021741
X-RAY DIFFRACTIONr_scbond_other5.377.6041742
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.81214.372509
X-RAY DIFFRACTIONr_long_range_B_refined8.93641.384043
X-RAY DIFFRACTIONr_long_range_B_other8.89838.243952
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.506→1.545 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 17 -
Rwork0.332 283 -
obs--6.04 %

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