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- PDB-8p5h: Kinase domain of mutant human ULK1 in complex with compound CCT241533 -

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Basic information

Entry
Database: PDB / ID: 8p5h
TitleKinase domain of mutant human ULK1 in complex with compound CCT241533
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE / Autophagy / Unc-like 1 kinase
Function / homology
Function and homology information


omegasome membrane / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / axon extension ...omegasome membrane / neuron projection regeneration / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / RAB GEFs exchange GTP for GDP on RABs / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / TBC/RABGAPs / reticulophagy / Receptor Mediated Mitophagy / Macroautophagy / cellular response to stress / response to starvation / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / cellular response to nutrient levels / negative regulation of protein-containing complex assembly / mitophagy / positive regulation of autophagy / autophagosome / macroautophagy / Regulation of TNFR1 signaling / recycling endosome / small GTPase binding / autophagy / neuron projection development / protein localization / peptidyl-serine phosphorylation / GTPase binding / protein autophosphorylation / mitochondrial outer membrane / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / regulation of autophagy / protein phosphorylation / axon / negative regulation of cell population proliferation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / protein-containing complex binding / signal transduction / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Serine/threonine-protein kinase, Ulk1/Ulk2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / : / Atg1-like, MIT domain 1 / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-XBJ / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsBattista, T. / Semrau, M.S. / Heroux, A. / Lolli, G. / Storici, P.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Crystal structures of ULK1 in complex with KCGS compounds
Authors: Battista, T. / Semrau, M.S. / Lolli, G. / Storici, P.
History
DepositionMay 24, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK1
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,27010
Polymers64,2422
Non-polymers1,0288
Water6,269348
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6355
Polymers32,1211
Non-polymers5144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6355
Polymers32,1211
Non-polymers5144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.650, 96.310, 109.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 8 - 280 / Label seq-ID: 9 - 281

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Serine/threonine-protein kinase ULK1 / Autophagy-related protein 1 homolog / ATG1 / hATG1 / Unc-51-like kinase 1


Mass: 32121.098 Da / Num. of mol.: 2 / Mutation: R245A, E246A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK1, KIAA0722 / Production host: Escherichia coli (E. coli)
References: UniProt: O75385, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-XBJ / 4-FLUORO-2-(4-{[(3S,4R)-4-(1-HYDROXY-1-METHYLETHYL)PYRROLIDIN-3-YL]AMINO}-6,7-DIMETHOXYQUINAZOLIN-2-YL)PHENOL


Mass: 442.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27FN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.46 Å3/Da / Density % sol: 64.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.941→66.9 Å / Num. obs: 66660 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Net I/σ(I): 16.9
Reflection shellResolution: 1.941→1.974 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3287 / CC1/2: 0.682 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.941→66.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.754 / SU ML: 0.077 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.193 3377 5.066 %
Rwork0.1698 63281 -
all0.171 --
obs-66658 99.97 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.553 Å2
Baniso -1Baniso -2Baniso -3
1--0.564 Å20 Å2-0 Å2
2--0.148 Å20 Å2
3---0.417 Å2
Refinement stepCycle: LAST / Resolution: 1.941→66.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 70 348 4714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124557
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164434
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.6516177
X-RAY DIFFRACTIONr_angle_other_deg0.5271.57810216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9075562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.628533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.55710833
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.62410203
X-RAY DIFFRACTIONr_chiral_restr0.0830.2684
X-RAY DIFFRACTIONr_chiral_restr_other0.020.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025249
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
X-RAY DIFFRACTIONr_nbd_refined0.2240.2848
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23907
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22250
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0170.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0830.211
X-RAY DIFFRACTIONr_nbd_other0.1630.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.219
X-RAY DIFFRACTIONr_mcbond_it3.5333.4112187
X-RAY DIFFRACTIONr_mcbond_other3.5343.4112187
X-RAY DIFFRACTIONr_mcangle_it4.4716.0832738
X-RAY DIFFRACTIONr_mcangle_other4.4726.0862739
X-RAY DIFFRACTIONr_scbond_it5.1383.9832370
X-RAY DIFFRACTIONr_scbond_other5.1373.9832371
X-RAY DIFFRACTIONr_scangle_it7.737.0413427
X-RAY DIFFRACTIONr_scangle_other7.7297.0413428
X-RAY DIFFRACTIONr_lrange_it8.91433.8145188
X-RAY DIFFRACTIONr_lrange_other8.87433.1975105
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.058678
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.08750.05008
12AX-RAY DIFFRACTIONLocal ncs0.08750.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.941-1.9910.2812350.2594615X-RAY DIFFRACTION99.9794
1.991-2.0450.2512430.2344497X-RAY DIFFRACTION99.8946
2.045-2.1050.2412370.2074379X-RAY DIFFRACTION99.8918
2.105-2.1690.2132380.1894260X-RAY DIFFRACTION100
2.169-2.240.2052100.1784141X-RAY DIFFRACTION100
2.24-2.3190.1842090.174002X-RAY DIFFRACTION100
2.319-2.4060.2171980.1813883X-RAY DIFFRACTION100
2.406-2.5050.2161800.1713727X-RAY DIFFRACTION99.9488
2.505-2.6160.2091970.1823573X-RAY DIFFRACTION100
2.616-2.7430.2021990.1663410X-RAY DIFFRACTION100
2.743-2.8910.2071680.1683274X-RAY DIFFRACTION100
2.891-3.0660.2141630.1693102X-RAY DIFFRACTION100
3.066-3.2780.2081690.1682898X-RAY DIFFRACTION100
3.278-3.5390.1891430.1722745X-RAY DIFFRACTION100
3.539-3.8760.2111360.1622509X-RAY DIFFRACTION100
3.876-4.3320.1641110.1432299X-RAY DIFFRACTION100
4.332-4.9990.1471180.1332035X-RAY DIFFRACTION99.9536
4.999-6.1130.19880.1771746X-RAY DIFFRACTION100
6.113-8.610.163870.1621369X-RAY DIFFRACTION100
8.61-66.90.138480.182817X-RAY DIFFRACTION99.5397

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