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- PDB-8p5l: Kinase domain of mutant human ULK1 in complex with compound MRT67307 -

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Basic information

Entry
Database: PDB / ID: 8p5l
TitleKinase domain of mutant human ULK1 in complex with compound MRT67307
ComponentsSerine/threonine-protein kinase ULK1
KeywordsTRANSFERASE / Autophagy / Unc-like 1 kinase / KCGS
Function / homology
Function and homology information


omegasome membrane / neuron projection regeneration / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / RAB GEFs exchange GTP for GDP on RABs / piecemeal microautophagy of the nucleus / regulation of tumor necrosis factor-mediated signaling pathway ...omegasome membrane / neuron projection regeneration / regulation of protein lipidation / negative regulation of collateral sprouting / Atg1/ULK1 kinase complex / positive regulation of autophagosome assembly / phagophore assembly site membrane / RAB GEFs exchange GTP for GDP on RABs / piecemeal microautophagy of the nucleus / regulation of tumor necrosis factor-mediated signaling pathway / axon extension / phagophore assembly site / reticulophagy / TBC/RABGAPs / autophagy of mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / response to starvation / autophagosome membrane / autophagosome assembly / regulation of macroautophagy / negative regulation of protein-containing complex assembly / cellular response to nutrient levels / positive regulation of autophagy / autophagosome / macroautophagy / peptidyl-threonine phosphorylation / Regulation of TNFR1 signaling / recycling endosome / autophagy / small GTPase binding / neuron projection development / protein localization / GTPase binding / peptidyl-serine phosphorylation / mitochondrial outer membrane / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / negative regulation of cell population proliferation / axon / 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-1FV / Serine/threonine-protein kinase ULK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.836 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 20, 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

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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)65,2698
Polymers64,2422
Non-polymers1,0266
Water8,035446
1
A: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6344
Polymers32,1211
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase ULK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6344
Polymers32,1211
Non-polymers5133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.600, 152.600, 206.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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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-1FV / N-{3-[(5-cyclopropyl-2-{[3-(morpholin-4-ylmethyl)phenyl]amino}pyrimidin-4-yl)amino]propyl}cyclobutanecarboxamide / MRT67307


Mass: 464.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H36N6O2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / 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: 3.6 Å3/Da / Density % sol: 65.79 %
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: 1.836→111.255 Å / Num. obs: 79997 / % possible obs: 99.5 % / Redundancy: 18.4 % / CC1/2: 1 / Net I/σ(I): 20.2
Reflection shellResolution: 1.836→1.867 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3987 / CC1/2: 0.81

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.836→111.255 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.611 / SU ML: 0.075 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.101
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2113 4146 5.183 %
Rwork0.1756 75851 -
all0.177 --
obs-79997 99.545 %
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: 32.223 Å2
Baniso -1Baniso -2Baniso -3
1--0.235 Å2-0.118 Å2-0 Å2
2---0.235 Å2-0 Å2
3---0.762 Å2
Refinement stepCycle: LAST / Resolution: 1.836→111.255 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 72 446 4814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0124628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164548
X-RAY DIFFRACTIONr_angle_refined_deg1.6631.6556282
X-RAY DIFFRACTIONr_angle_other_deg0.5541.57810500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0695583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.457529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95610850
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.16510205
X-RAY DIFFRACTIONr_chiral_restr0.0830.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025346
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021074
X-RAY DIFFRACTIONr_nbd_refined0.2220.2890
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.24011
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22224
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2440.2347
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0770.214
X-RAY DIFFRACTIONr_nbd_other0.1890.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0970.226
X-RAY DIFFRACTIONr_mcbond_it3.4493.1182203
X-RAY DIFFRACTIONr_mcbond_other3.4493.1182203
X-RAY DIFFRACTIONr_mcangle_it4.7615.5692761
X-RAY DIFFRACTIONr_mcangle_other4.765.5712762
X-RAY DIFFRACTIONr_scbond_it4.6843.6672425
X-RAY DIFFRACTIONr_scbond_other4.6833.6692426
X-RAY DIFFRACTIONr_scangle_it7.2126.4623486
X-RAY DIFFRACTIONr_scangle_other7.2116.4643487
X-RAY DIFFRACTIONr_lrange_it9.19530.2025263
X-RAY DIFFRACTIONr_lrange_other9.11929.2355121
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.836-1.8830.3143390.27955340.28158770.9380.9599.93190.263
1.883-1.9350.3952820.38352560.38457550.9050.90296.22940.363
1.935-1.9910.2713040.23453280.23656360.950.96399.9290.205
1.991-2.0520.252450.20251460.20553920.960.97399.98150.175
2.052-2.1190.2532740.23649650.23752830.9530.95999.16710.201
2.119-2.1940.2272660.18148270.18450930.9660.9791000.155
2.194-2.2770.3152400.23946120.24249400.9320.9698.21860.199
2.277-2.3690.2022420.17544920.17747340.9740.9811000.151
2.369-2.4750.2132230.16443300.16745530.9710.9831000.143
2.475-2.5950.2042110.16241510.16443620.9770.9841000.142
2.595-2.7360.2182250.16739140.1741390.970.9831000.149
2.736-2.9020.2122190.1737060.17339250.9710.9821000.157
2.902-3.1020.1982040.16635040.16837080.9770.9841000.161
3.102-3.350.21900.17332530.17434430.9750.9841000.17
3.35-3.670.2031690.17530010.17731720.980.98699.9370.178
3.67-4.1020.1591460.1427520.14129020.9850.98999.86220.15
4.102-4.7360.151130.12224530.12325660.9870.9911000.139
4.736-5.7970.2151170.15620570.15921740.9830.991000.175
5.797-8.1880.196860.16716300.16917160.9810.9871000.188
8.188-111.2550.169510.1639400.1639930.980.98499.79860.201

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