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- PDB-9qb5: AP2-associated protein kinase 1 (AAK1) bound to CKJB68 -

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Basic information

Entry
Database: PDB / ID: 9qb5
TitleAP2-associated protein kinase 1 (AAK1) bound to CKJB68
ComponentsAP2-associated protein kinase 1
KeywordsTRANSFERASE / Kinase Inhibitor Macrocycle
Function / homology
Function and homology information


regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / membrane organization / Notch binding / clathrin-coated vesicle / positive regulation of Notch signaling pathway / presynaptic endocytosis / cell leading edge / clathrin-coated pit / terminal bouton ...regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / membrane organization / Notch binding / clathrin-coated vesicle / positive regulation of Notch signaling pathway / presynaptic endocytosis / cell leading edge / clathrin-coated pit / terminal bouton / Cargo recognition for clathrin-mediated endocytosis / presynapse / regulation of protein localization / Clathrin-mediated endocytosis / 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 / protein stabilization / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / ATP binding / plasma membrane / cytosol
Similarity search - Function
: / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-F7I / AP2-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPreuss, F. / Mensing, T.E. / Hanke, T. / Knapp, S. / Mathea, S.
Funding support Germany, 1items
OrganizationGrant numberCountry
Not funded Germany
CitationJournal: To Be Published
Title: AP2-associated protein kinase 1 (AAK1) bound to CKJB68
Authors: Preuss, F. / Mensing, T.E. / Hanke, T. / Knapp, S. / Mathea, S.
History
DepositionFeb 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP2-associated protein kinase 1
B: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0909
Polymers71,7512
Non-polymers1,3397
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-62 kcal/mol
Surface area26990 Å2
Unit cell
Length a, b, c (Å)74.386, 74.386, 260.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein AP2-associated protein kinase 1 / Adaptor-associated kinase 1


Mass: 35875.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAK1, KIAA1048 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2M2I8, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-F7I / ~{N}-(phenylmethyl)-7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaene-5-carboxamide


Mass: 429.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M ammonium sulfate 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.82→49 Å / Num. obs: 66978 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 36.47 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.7
Reflection shellResolution: 1.82→1.86 Å / Redundancy: 10.2 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3859 / CC1/2: 0.626 / % possible all: 99.3

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→44.99 Å / SU ML: 0.2725 / Cross valid method: FREE R-VALUE / σ(F): 1.63 / Phase error: 21.4214
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2528 4.99 %
Rwork0.1979 48092 -
obs0.1994 50620 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.07 Å2
Refinement stepCycle: LAST / Resolution: 2→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4776 0 89 149 5014
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724965
X-RAY DIFFRACTIONf_angle_d0.82826751
X-RAY DIFFRACTIONf_chiral_restr0.0554761
X-RAY DIFFRACTIONf_plane_restr0.0065914
X-RAY DIFFRACTIONf_dihedral_angle_d6.2339739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.40841480.36022582X-RAY DIFFRACTION100
2.04-2.080.33961480.30442624X-RAY DIFFRACTION99.96
2.08-2.130.31171490.25042618X-RAY DIFFRACTION100
2.13-2.170.25331300.21322610X-RAY DIFFRACTION99.96
2.17-2.230.24741350.20312601X-RAY DIFFRACTION100
2.23-2.290.22751590.1952644X-RAY DIFFRACTION100
2.29-2.360.23051080.20912638X-RAY DIFFRACTION100
2.36-2.430.26641210.20992661X-RAY DIFFRACTION100
2.43-2.520.24051530.22042639X-RAY DIFFRACTION100
2.52-2.620.26821550.2242618X-RAY DIFFRACTION100
2.62-2.740.25911310.21442667X-RAY DIFFRACTION100
2.74-2.880.32971590.21832642X-RAY DIFFRACTION100
2.88-3.070.26051260.22182682X-RAY DIFFRACTION100
3.07-3.30.24491430.22562696X-RAY DIFFRACTION100
3.3-3.630.20951520.20192687X-RAY DIFFRACTION100
3.63-4.160.19891340.16672740X-RAY DIFFRACTION100
4.16-5.240.14511530.15312761X-RAY DIFFRACTION100
5.24-44.990.20761240.17812982X-RAY DIFFRACTION99.94
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)
15.890850981811.009386535011.383155817920.7819161430560.556396442581.222936193930.0211796638591-0.00543375873249-0.1645842533270.06386560888640.007977815527380.08834682618240.1722915332950.0425448251108-0.01532677017030.327054046071-0.0135922357988-0.04378404963350.1875164674970.01135805858390.24094900508622.520009808830.662597968218.6302107312
22.088553079570.3091676321170.1896194122081.916694760450.3887198664083.8727647879-0.0290872979472-0.0508304906555-0.001041288187120.01618250231920.0716569848659-0.02349433067960.280810365845-0.00140938149002-0.02745784067780.2659185284710.0127256835022-0.02967585708490.198352219082-0.03138706013660.22019633953139.986810581734.45990826335.5723341041
32.472360802650.4930599846470.03555120889883.28543418616-0.1826592990814.269482480760.1168337638770.479408452610.313472049889-0.1246236068320.07085069782660.634163613452-0.0616008123553-0.957741044502-0.1617321994810.277265127771-0.03058461309320.006841776815910.5295664469690.04028619571670.41450069662515.12383441975.27613920656-9.20737224714
43.2183757124-0.03939556737362.122712062851.142193182840.07719197314492.585542269430.2124627076970.0641274164195-0.06591923682650.05143488808070.03630007479780.0134784654431-0.04419709400160.0838122061121-0.2672682203790.206693595058-0.03269546141930.0271027906250.3071778579250.04015570082340.25669337067326.03705861520.390106092747-5.94639374455
52.338241797770.04765005287840.3449238213311.471260168490.2943871129723.448008911830.00388684352944-0.006386051949590.08315610008780.0784233985053-0.078633545482-0.109752826337-0.3024215635930.1595389447290.05510475834720.23567403686-0.0599881236346-0.04269856073760.2480104669990.03996124632070.25217893595445.63089314842.55639738022.49241030861
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 34 through 147 )BB34 - 1471 - 114
22chain 'B' and (resid 148 through 342 )BB148 - 342115 - 309
33chain 'A' and (resid 28 through 69 )AA28 - 691 - 42
44chain 'A' and (resid 70 through 147 )AA70 - 14743 - 120
55chain 'A' and (resid 148 through 343 )AA148 - 343121 - 314

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