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- PDB-6qat: Crystal structure of ULK2 in complexed with hesperadin -

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Basic information

Entry
Database: PDB / ID: 6qat
TitleCrystal structure of ULK2 in complexed with hesperadin
ComponentsSerine/threonine-protein kinase ULK2
KeywordsTRANSFERASE / ULK2 / autophagy / kinase / inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of collateral sprouting / collateral sprouting / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / axon extension / phagophore assembly site / reticulophagy / autophagy of mitochondrion / response to starvation / autophagosome assembly ...negative regulation of collateral sprouting / collateral sprouting / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / axon extension / phagophore assembly site / reticulophagy / autophagy of mitochondrion / response to starvation / autophagosome assembly / positive regulation of autophagy / autophagosome / cytoplasmic vesicle membrane / autophagy / protein autophosphorylation / non-specific serine/threonine protein kinase / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FE7 / Serine/threonine-protein kinase ULK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsChaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.J. / Year: 2019
Title: Conservation of structure, function and inhibitor binding in UNC-51-like kinase 1 and 2 (ULK1/2).
Authors: Chaikuad, A. / Koschade, S.E. / Stolz, A. / Zivkovic, K. / Pohl, C. / Shaid, S. / Ren, H. / Lambert, L.J. / Cosford, N.D.P. / Brandts, C.H. / Knapp, S.
History
DepositionDec 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase ULK2
B: Serine/threonine-protein kinase ULK2
C: Serine/threonine-protein kinase ULK2
D: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1388
Polymers127,0714
Non-polymers2,0674
Water32418
1
A: Serine/threonine-protein kinase ULK2
hetero molecules

B: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5694
Polymers63,5352
Non-polymers1,0332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area3930 Å2
ΔGint-23 kcal/mol
Surface area24300 Å2
MethodPISA
2
C: Serine/threonine-protein kinase ULK2
hetero molecules

D: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5694
Polymers63,5352
Non-polymers1,0332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_344-x-2,y-1/2,-z-11
Buried area4280 Å2
ΔGint-26 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.208, 77.561, 94.941
Angle α, β, γ (deg.)90.00, 97.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLYGLYAA1 - 2745 - 278
21METMETGLYGLYBB1 - 2745 - 278
12METMETGLNGLNAA1 - 2735 - 277
22METMETGLNGLNCC1 - 2735 - 277
13METMETPROPROAA1 - 2695 - 273
23METMETPROPRODD1 - 2695 - 273
14SERSERGLNGLNBB0 - 2734 - 277
24SERSERGLNGLNCC0 - 2734 - 277
15METMETPHEPHEBB1 - 2705 - 274
25METMETPHEPHEDD1 - 2705 - 274
16METMETPROPROCC1 - 2695 - 273
26METMETPROPRODD1 - 2695 - 273

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Serine/threonine-protein kinase ULK2 / Unc-51-like kinase 2


Mass: 31767.721 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ULK2, KIAA0623 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pARE2
References: UniProt: Q8IYT8, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-FE7 / N-{(3Z)-2-oxo-3-[phenyl({4-[(piperidin-1-yl)methyl]phenyl}amino)methylidene]-2,3-dihydro-1H-indol-5-yl}ethanesulfonamide


Mass: 516.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H32N4O3S / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 27.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.75, 5% glycerol
PH range: 5.75-5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→48.75 Å / Num. obs: 27487 / % possible obs: 99.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 82 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.1
Reflection shellResolution: 2.77→2.92 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.758 / Mean I/σ(I) obs: 2 / Num. unique obs: 4001 / CC1/2: 0.884 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNO

4wno


Resolution: 2.77→48.75 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 46.344 / SU ML: 0.427 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 1357 4.9 %RANDOM
Rwork0.21776 ---
obs0.21993 26116 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 108.746 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å2-1.81 Å2
2--0.82 Å2-0 Å2
3----3.28 Å2
Refinement stepCycle: 1 / Resolution: 2.77→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8141 0 148 18 8307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138480
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178010
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.6311432
X-RAY DIFFRACTIONr_angle_other_deg1.0331.59818545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.81251000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.95422.067445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.867151504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1711554
X-RAY DIFFRACTIONr_chiral_restr0.0380.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029878
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021836
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_it2.9875.3074047
X-RAY DIFFRACTIONr_mcbond_other2.9875.3074046
X-RAY DIFFRACTIONr_mcangle_it4.7617.9525030
X-RAY DIFFRACTIONr_mcangle_other4.7617.9535031
X-RAY DIFFRACTIONr_scbond_it3.0815.674433
X-RAY DIFFRACTIONr_scbond_other3.0815.6724434
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9978.3966403
X-RAY DIFFRACTIONr_long_range_B_refined7.18960.799005
X-RAY DIFFRACTIONr_long_range_B_other7.18960.7859005
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73970.07
12B73970.07
21A79510.07
22C79510.07
31A77430.07
32D77430.07
41B74000.06
42C74000.06
51B71910.07
52D71910.07
61C78150.06
62D78150.06
LS refinement shellResolution: 2.77→2.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 101 -
Rwork0.327 1900 -
obs--99.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.73410.82620.56765.7616-0.03786.67520.2608-0.0144-0.30161.0336-0.3826-0.09460.3470.12950.12180.2271-0.1208-0.01590.2034-0.0070.0393-28.560813.5433-75.6478
22.8977-4.5367-1.2277.56942.54032.5824-0.2585-0.21331.10880.90480.1191-1.76-0.25380.30650.13941.0443-0.6284-0.57210.64040.16470.6996-21.308828.1777-60.6431
33.89510.5445-0.034310.1589-2.89997.35320.0509-1.2191-0.34392.4398-0.1098-0.5-0.24930.85790.05891.2678-0.3074-0.50130.94650.16030.3698-18.607618.4911-52.2993
43.7231-0.3334-0.11166.87724.19486.82380.2437-0.67560.0609-0.3816-0.58640.0504-0.476-0.3070.34260.09060.02540.01880.29060.04970.0657-30.84064.9266-0.0551
50.9392-0.3471.04786.17180.10535.650.134-0.08420.1865-0.9534-0.1994-0.3894-0.89940.34250.06540.46030.08720.18560.38920.10680.1583-25.849910.0074-16.2411
61.80843.97350.208111.7033-1.20431.1156-0.35560.23910.0096-1.00640.2263-0.3984-0.25690.15880.12931.06520.20610.18640.50350.09790.1579-29.969912.1632-34.0303
70.96791.38860.64652.7284-0.53075.3930.03520.1777-0.07310.00440.41210.05260.34350.3064-0.44730.0563-0.05340.06790.90340.01650.6983-64.78072.1593-81.5703
85.02232.4816-0.52688.0177-1.63616.5712-0.002-0.53220.0321.42470.26710.1753-0.07990.2062-0.26520.4672-0.0050.24760.7585-0.13920.3829-55.85879.5176-61.0018
95.1809-1.66583.14353.3866-0.8236.7960.07370.3640.0838-0.19720.1891-0.05460.5544-0.1215-0.26280.2886-0.1093-0.00140.8282-0.01860.2619-64.305810.0416-21.1277
100.6652-1.9495-0.67198.2450.99661.32630.07490.13980.0817-1.21180.08270.38850.1132-0.1026-0.15760.5919-0.2097-0.25331.15330.05170.5171-76.34516.7365-41.0586
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 165
2X-RAY DIFFRACTION2A166 - 211
3X-RAY DIFFRACTION3A212 - 274
4X-RAY DIFFRACTION4B-3 - 52
5X-RAY DIFFRACTION5B53 - 165
6X-RAY DIFFRACTION6B166 - 274
7X-RAY DIFFRACTION7C0 - 186
8X-RAY DIFFRACTION8C187 - 273
9X-RAY DIFFRACTION9D1 - 163
10X-RAY DIFFRACTION10D164 - 270

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