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- PDB-6qav: Crystal structure of ULK2 in complexed with MRT68921 -

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Basic information

Entry
Database: PDB / ID: 6qav
TitleCrystal structure of ULK2 in complexed with MRT68921
ComponentsSerine/threonine-protein kinase ULK2
KeywordsTRANSFERASE / ULK2 / autophagy / kinase / inhibitor complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


somatic sensory system development / negative regulation of collateral sprouting / collateral sprouting / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / axon extension / reticulophagy / response to starvation / autophagosome assembly ...somatic sensory system development / negative regulation of collateral sprouting / collateral sprouting / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / axon extension / reticulophagy / response to starvation / autophagosome assembly / mitophagy / axon guidance / autophagosome / cytoplasmic vesicle membrane / autophagy / intracellular protein localization / protein autophosphorylation / non-specific serine/threonine protein kinase / regulation of autophagy / 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-HVH / Serine/threonine-protein kinase ULK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsChaikuad, A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / 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
Revision 1.3Oct 15, 2025Group: Structure summary / Category: audit_author / pdbx_entry_details

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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)129,94726
Polymers127,0714
Non-polymers2,87722
Water6,431357
1
A: Serine/threonine-protein kinase ULK2
B: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,01614
Polymers63,5352
Non-polymers1,48112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-33 kcal/mol
Surface area24780 Å2
MethodPISA
2
C: Serine/threonine-protein kinase ULK2
D: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,93112
Polymers63,5352
Non-polymers1,39610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-23 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.648, 69.050, 107.710
Angle α, β, γ (deg.)90.00, 97.93, 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
11SERSERGLUGLUAA0 - 2724 - 276
21SERSERGLUGLUBB0 - 2724 - 276
12METMETLEULEUAA1 - 2715 - 275
22METMETLEULEUCC1 - 2715 - 275
13METMETGLUGLUAA1 - 2725 - 276
23METMETGLUGLUDD1 - 2725 - 276
14METMETGLNGLNBB1 - 2735 - 277
24METMETGLNGLNCC1 - 2735 - 277
15METMETGLUGLUBB1 - 2725 - 276
25METMETGLUGLUDD1 - 2725 - 276
16METMETGLUGLUCC1 - 2725 - 276
26METMETGLUGLUDD1 - 2725 - 276

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#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-pRARE2
References: UniProt: Q8IYT8, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 379 molecules

#2: Chemical
ChemComp-HVH / ~{N}-[3-[[5-cyclopropyl-2-[(2-methyl-3,4-dihydro-1~{H}-isoquinolin-6-yl)amino]pyrimidin-4-yl]amino]propyl]cyclobutanecarboxamide


Mass: 434.577 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H34N6O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 43.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 37.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.5, 5% glycerol
PH range: 5.5-5.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→57.97 Å / Num. obs: 68365 / % possible obs: 100 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 11.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.657 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 6706 / CC1/2: 0.842 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WNO

4wno


Resolution: 2.05→57.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 12.057 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.233 / ESU R Free: 0.181 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23085 3331 4.9 %RANDOM
Rwork0.19518 ---
obs0.19696 65014 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å2-0.38 Å2
2--2.79 Å20 Å2
3----1.88 Å2
Refine analyzeLuzzati coordinate error obs: 0.292 Å
Refinement stepCycle: 1 / Resolution: 2.05→57.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8578 0 201 357 9136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0149050
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178337
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.64512182
X-RAY DIFFRACTIONr_angle_other_deg0.9051.66819539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88351087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75921.929477
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.276151616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8771561
X-RAY DIFFRACTIONr_chiral_restr0.0710.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021682
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_it1.8512.2924320
X-RAY DIFFRACTIONr_mcbond_other1.8512.2914311
X-RAY DIFFRACTIONr_mcangle_it3.1043.4255391
X-RAY DIFFRACTIONr_mcangle_other3.1043.4255392
X-RAY DIFFRACTIONr_scbond_it1.9822.5614730
X-RAY DIFFRACTIONr_scbond_other1.9822.5614730
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1923.7176764
X-RAY DIFFRACTIONr_long_range_B_refined6.56926.4159812
X-RAY DIFFRACTIONr_long_range_B_other6.56926.429813
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)
11A81400.1
12B81400.1
21A81750.11
22C81750.11
31A77510.1
32D77510.1
41B82670.11
42C82670.11
51B76170.11
52D76170.11
61C76840.11
62D76840.11
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 238 -
Rwork0.3 4818 -
obs--99.76 %
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)
11.7395-0.4106-0.19120.18990.11150.5155-0.0289-0.0127-0.1319-0.0299-0.01370.016-0.0788-0.16560.04260.24770.00760.05150.2153-0.00320.0887-99.9723-8.3988-55.6092
22.97260.82-1.38260.61230.46773.14190.1443-0.9197-0.0595-0.1103-0.0632-0.0624-0.18990.6666-0.08120.2374-0.05680.03660.56360.0260.0125-97.6586-3.2349-33.8583
31.2531-0.60670.12420.45810.19390.61380.0805-0.0114-0.00750.0063-0.05260.01090.061-0.0061-0.02790.2837-0.00080.01780.1680.00330.0914-68.8148-16.3554-58.0287
42.8573-0.1335-0.17350.64290.7682.9351-0.117-0.4344-0.02240.17030.07790.06820.2129-0.26110.03910.36430.0029-0.00050.27010.02750.0098-66.7696-20.8106-36.1199
50.9993-0.02490.08980.398-0.33421.251-0.01830.10720.01080.11130.0149-0.1241-0.0625-0.05310.00340.19670.01510.02990.24730.02180.1189-101.9783-10.07637.6467
61.1733-0.04330.61141.7392-0.48222.04410.02820.4467-0.0506-0.1055-0.0091-0.15730.12120.0491-0.01920.1278-0.00670.05170.45270.03180.0448-104.6579-10.1229-14.3666
73.5028-0.86710.32330.2692-0.19510.791-0.19040.0807-0.04210.0990.04470.0049-0.06160.08930.14580.20880.03960.01380.2014-0.00220.1414-70.2389-18.22684.9297
85.6407-0.62361.66682.1603-1.00132.63130.07311.64280.35460.0014-0.33340.2411-0.23210.75380.26030.1882-0.0381-0.04240.78830.10040.1193-68.17-16.887-17.3724
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 187
2X-RAY DIFFRACTION2A188 - 272
3X-RAY DIFFRACTION3B0 - 187
4X-RAY DIFFRACTION4B188 - 273
5X-RAY DIFFRACTION5C1 - 187
6X-RAY DIFFRACTION6C188 - 275
7X-RAY DIFFRACTION7D1 - 188
8X-RAY DIFFRACTION8D189 - 272

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