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- PDB-8a5x: Crystal structure of phosphatidyl inositol 4-kinase II beta in co... -

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Basic information

Entry
Database: PDB / ID: 8a5x
TitleCrystal structure of phosphatidyl inositol 4-kinase II beta in complex with MM1373
ComponentsPhosphatidylinositol 4-kinase type 2-beta,Endolysin
KeywordsTRANSFERASE / lipid / kinase / PI4K2B / inhibitor
Function / homology
Function and homology information


Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...Synthesis of PIPs at the ER membrane / 1-phosphatidylinositol 4-kinase / 1-phosphatidylinositol 4-kinase activity / Synthesis of PIPs at the early endosome membrane / Synthesis of PIPs at the Golgi membrane / endosome organization / phosphatidylinositol biosynthetic process / Golgi organization / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / viral release from host cell by cytolysis / peptidoglycan catabolic process / trans-Golgi network / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / early endosome membrane / host cell cytoplasm / endosome / defense response to bacterium / phosphorylation / Golgi membrane / endoplasmic reticulum membrane / ATP binding / membrane / plasma membrane / cytosol
Similarity search - Function
Type II phosphatidylinositol 4-kinase Lsb6/PI4K2 / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Chem-L6A / Endolysin / Phosphatidylinositol 4-kinase type 2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKlima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2022
Title: Structure-based design and modular synthesis of novel PI4K class II inhibitors bearing a 4-aminoquinazoline scaffold.
Authors: Misehe, M. / Klima, M. / Matousova, M. / Chalupska, D. / Dejmek, M. / Sala, M. / Mertlikova-Kaiserova, H. / Boura, E. / Nencka, R.
History
DepositionJun 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 19, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
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 4-kinase type 2-beta,Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6622
Polymers59,3681
Non-polymers2941
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.383, 87.007, 71.376
Angle α, β, γ (deg.)90.000, 107.780, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Phosphatidylinositol 4-kinase type 2-beta,Endolysin / Phosphatidylinositol 4-kinase type II-beta / PI4KII-BETA / Lysis protein / Lysozyme / Muramidase


Mass: 59367.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PI4K2B / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8TCG2, UniProt: P00720, 1-phosphatidylinositol 4-kinase, lysozyme
#2: Chemical ChemComp-L6A / 4-azanyl-7-[3-(hydroxymethyl)phenyl]quinazoline-6-carboxamide


Mass: 294.308 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H14N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 10% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO, 100 mM bicine/Trizma base pH 8.5, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4- ...Details: 10% w/v PEG 8.000, 20% v/v ethylene glycol, 3% v/v DMSO, 100 mM bicine/Trizma base pH 8.5, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.4→31.63 Å / Num. obs: 20410 / % possible obs: 92.17 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.31 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.09953 / Rpim(I) all: 0.05996 / Rrim(I) all: 0.1164 / Net I/σ(I): 13.38
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.6079 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 1863 / CC1/2: 0.764 / CC star: 0.931 / Rpim(I) all: 0.3578 / Rrim(I) all: 0.7059 / % possible all: 84.38

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Processing

Software
NameVersionClassification
XDSxdsgui2data reduction
XDSxdsgui2data scaling
PHASER2.8.3phasing
Coot0.9.6model building
PHENIX1.20_4459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WTV

4wtv


Resolution: 2.4→31.63 Å / SU ML: 0.2735 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1020 5 %random selection
Rwork0.2105 19382 --
obs0.2115 20402 92.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3781 0 22 106 3909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223894
X-RAY DIFFRACTIONf_angle_d0.4775268
X-RAY DIFFRACTIONf_chiral_restr0.0402560
X-RAY DIFFRACTIONf_plane_restr0.0039702
X-RAY DIFFRACTIONf_dihedral_angle_d10.87761470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.530.29421340.26282541X-RAY DIFFRACTION84.89
2.53-2.680.27881390.25932667X-RAY DIFFRACTION89.25
2.68-2.890.29351500.24932839X-RAY DIFFRACTION95.25
2.89-3.180.22851500.2382864X-RAY DIFFRACTION95.47
3.18-3.640.23531510.22242872X-RAY DIFFRACTION96.09
3.64-4.590.20011500.17742843X-RAY DIFFRACTION94.6
4.59-31.630.20561460.17772756X-RAY DIFFRACTION90.1

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