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- PDB-6qau: Crystal structure of ULK2 in complexed with MRT67307 -

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Basic information

Entry
Database: PDB / ID: 6qau
TitleCrystal structure of ULK2 in complexed with MRT67307
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 / phagophore assembly site / axon extension / reticulophagy / response to starvation / autophagosome assembly / autophagosome ...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 / autophagosome / positive regulation of autophagy / 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 / : / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / 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 / : / ATG1-like, MIT domain 2 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / 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-1FV / Serine/threonine-protein kinase ULK2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,38317
Polymers95,3033
Non-polymers2,08014
Water3,135174
1
A: Serine/threonine-protein kinase ULK2
hetero molecules

A: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,21616
Polymers63,5352
Non-polymers1,68114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area8200 Å2
ΔGint-41 kcal/mol
Surface area25590 Å2
MethodPISA
2
B: Serine/threonine-protein kinase ULK2
C: Serine/threonine-protein kinase ULK2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7759
Polymers63,5352
Non-polymers1,2407
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-11 kcal/mol
Surface area25320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.006, 117.006, 141.485
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11C-431-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYAA0 - 2744 - 278
21GLYGLYBB0 - 2744 - 278
12GLNGLNAA0 - 2734 - 277
22GLNGLNCC0 - 2734 - 277
13GLNGLNBB0 - 2734 - 277
23GLNGLNCC0 - 2734 - 277

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 31767.721 Da / Num. of mol.: 3
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, 188 molecules

#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.: 3 / Source method: obtained synthetically / Formula: C26H36N6O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 22.5% PEG 3350, 0.2 M sodium citrate, pH 5.9, 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: 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: 2.48→58.5 Å / Num. obs: 40240 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 47 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.136 / Net I/σ(I): 11.5
Reflection shellResolution: 2.48→2.61 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5786 / CC1/2: 0.711 / % possible all: 100

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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: 2.48→58.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.941 / SU ML: 0.217 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.25 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2366 2088 5.2 %RANDOM
Rwork0.19559 ---
obs0.19776 38110 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 57.774 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.35 Å2-0 Å2
2---0.69 Å20 Å2
3---2.25 Å2
Refine analyzeLuzzati coordinate error obs: 0.346 Å
Refinement stepCycle: 1 / Resolution: 2.48→58.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 145 174 6641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0146628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176054
X-RAY DIFFRACTIONr_angle_refined_deg1.121.6458917
X-RAY DIFFRACTIONr_angle_other_deg0.8531.66814180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0295790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.5121.813353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.849151164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8421546
X-RAY DIFFRACTIONr_chiral_restr0.060.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027556
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021236
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_it2.2853.3063169
X-RAY DIFFRACTIONr_mcbond_other2.2853.3073170
X-RAY DIFFRACTIONr_mcangle_it3.9994.943946
X-RAY DIFFRACTIONr_mcangle_other3.9984.943947
X-RAY DIFFRACTIONr_scbond_it2.1343.5643459
X-RAY DIFFRACTIONr_scbond_other2.1343.5643459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.715.1984954
X-RAY DIFFRACTIONr_long_range_B_refined6.72636.6867149
X-RAY DIFFRACTIONr_long_range_B_other6.72536.6957150
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)
11A79340.11
12B79340.11
21A73090.11
22C73090.11
31B75310.08
32C75310.08
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 139 -
Rwork0.292 2782 -
obs--99.83 %
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)
11.2606-0.56890.06082.2135-0.84461.1996-0.08150.06210.01810.0186-0.0408-0.06470.01330.10610.12220.107-0.05020.02970.15190.01790.214142.3356-43.1639-36.9238
22.77431.09061.3492.4563-0.31251.019-0.05350.18330.18060.20860.03660.1706-0.14560.07280.01690.17910.01630.03860.09830.06010.34130.9583-26.9281-40.4705
33.33530.1139-1.4090.9056-0.59561.74910.057-0.05420.36370.03380.1091-0.0034-0.0454-0.39-0.16610.05330.0166-0.03830.29330.0240.205215.2657-46.8193-2.6891
40.1651-0.4056-0.20753.17110.52710.6024-0.0595-0.10520.0923-0.01140.1315-0.3749-0.09870.0896-0.0720.15260.013-0.03250.1682-0.01140.333137.3536-41.3641-9.7827
54.23990.51320.51470.90910.24481.0266-0.12950.02840.1043-0.25960.05990.55830.0679-0.04810.06960.137-0.0239-0.1420.00850.03940.640912.5983-7.7476-5.8211
60.43060.6980.3356.22050.95660.321-0.10250.07560.0135-0.2730.1406-0.091-0.01870.0693-0.03810.21880.0207-0.02010.1232-0.00870.311232.7936-10.1187-1.679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 142
2X-RAY DIFFRACTION2A143 - 275
3X-RAY DIFFRACTION3B0 - 167
4X-RAY DIFFRACTION4B178 - 274
5X-RAY DIFFRACTION5C-1 - 141
6X-RAY DIFFRACTION6C142 - 273

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