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- PDB-5te0: Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) i... -

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Basic information

Entry
Database: PDB / ID: 5te0
TitleCrystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with BIBF 1120
ComponentsAP2-associated protein kinase 1
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


presynaptic endocytosis / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / membrane organization / Notch binding / clathrin-coated vesicle / positive regulation of Notch signaling pathway / cell leading edge / clathrin-coated pit / terminal bouton ...presynaptic endocytosis / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / membrane organization / Notch binding / clathrin-coated vesicle / positive regulation of Notch signaling pathway / cell leading edge / clathrin-coated pit / terminal bouton / regulation of protein localization / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-XIN / AP2-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCounago, R.M. / Elkins, J.M. / Bountra, C. / Arruda, P. / Edwards, A.M. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2013/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with BIBF 1120
Authors: Counago, R.M. / Elkins, J.M. / Arrowsmith, C.H. / Bountra, C. / Arruda, P. / Edwards, A.M. / Gileadi, O.
History
DepositionSep 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,46511
Polymers39,0831
Non-polymers1,38210
Water5,296294
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.465, 119.474, 125.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

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Components

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


Mass: 39082.836 Da / Num. of mol.: 1 / Fragment: UNP residues 27-365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAK1, KIAA1048 / Plasmid: pNIC-CTH0 / Production host: Escherichia coli (E. coli) / Strain (production host): DE3
References: UniProt: Q2M2I8, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-XIN / methyl (3Z)-3-{[(4-{methyl[(4-methylpiperazin-1-yl)acetyl]amino}phenyl)amino](phenyl)methylidene}-2-oxo-2,3-dihydro-1H-indole-6-carboxylate / Nintedanib


Mass: 539.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H33N5O4 / Comment: medication*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 3.37 Å3/Da / Density % sol: 63.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25 % PEG 3350, 0.1M BIS-TRIS, 0.2M Lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45872 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45872 Å / Relative weight: 1
ReflectionResolution: 1.9→43.55 Å / Num. obs: 41475 / % possible obs: 99.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 26.73 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.202 / Rsym value: 0.073 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.584 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.429 / % possible all: 93.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSVERSION Oct 15, 2015data reduction
Aimless0.5.27data scaling
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wsq

4wsq


Resolution: 1.9→19.15 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.911 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.112 / SU Rfree Blow DPI: 0.103 / SU Rfree Cruickshank DPI: 0.099
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2182 5.27 %RANDOM
Rwork0.181 ---
obs0.182 41423 98.9 %-
Displacement parametersBiso mean: 31.27 Å2
Baniso -1Baniso -2Baniso -3
1-9.777 Å20 Å20 Å2
2---7.6279 Å20 Å2
3----2.1491 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 1.9→19.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 95 294 2830
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015003HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.048999HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1105SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes64HARMONIC2
X-RAY DIFFRACTIONt_gen_planes773HARMONIC5
X-RAY DIFFRACTIONt_it5003HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion15.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion333SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5690SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 123 4.62 %
Rwork0.301 2538 -
all0.305 2661 -
obs--87.19 %
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)
16.48520.72043.87972.1260.26266.0358-0.1122-1.08880.14960.02770.25760.2598-0.0854-0.9558-0.1454-0.09470.00030.03710.15740.0911-0.236-8.9155-30.84232.3144
26.4837-5.821.08851.81725.075111.98480.0791-0.8336-0.24180.062-0.03890.24450.1398-0.7258-0.0402-0.1197-0.07590.04060.17110.0982-0.1949-12.577-33.0175-2.8782
33.15160.81460.91764.80045.03172.7373-0.0617-0.43940.64380.0880.01660.0053-0.70110.19060.04520.2232-0.0817-0.01260.0118-0.1016-0.0628-18.4257-18.4334-9.9986
44.44150.4786-0.18370.688-0.15140.89910.1298-0.8390.01810.1538-0.0440.12740.0059-0.0563-0.0858-0.0113-0.02050.0228-0.00590.0065-0.1433-12.4121-29.8306-10.9505
55.4934-1.2016-0.0780.54990.13510.5394-0.0042-0.12520.027-0.025-0.0327-0.06080.05590.03930.0369-0.0115-0.01140.0121-0.17130.0086-0.0796-1.4141-30.3267-24.8187
62.543-0.60020.27552.4459-0.07561.22990.0035-0.2440.11920.2032-0.04590.07710.0227-0.02440.04250.0022-0.02480.0304-0.1117-0.0191-0.0964-7.3712-24.2796-19.0737
71.0480.60261.2568.3271-1.98232.1142-0.0921-0.2040.68120.5065-0.35480.6178-0.3262-0.19340.44690.0950.0040.0171-0.0462-0.11690.2388-8.7264-3.8314-18.4757
81.60550.0922-0.08731.17270.250.48010.00360.06010.27810.0085-0.0193-0.0380.01090.01710.01570.0265-0.0088-0.0001-0.13050.0118-0.00962.6382-17.1834-28.4911
93.9032-0.01960.18720.8308-0.70020.8346-0.01350.5412-0.2455-0.16740.00630.06570.0519-0.00620.00730.0843-0.01370.0085-0.0267-0.0349-0.006-5.0402-28.5765-38.9288
102.3451-1.0139-2.48353.0531-0.25940.00250.01610.26430.4081-0.27110.026-0.4681-0.0761-0.2225-0.04210.0321-0.00560.0644-0.13350.02330.084316.6079-16.8468-36.1675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|26 - 63}
2X-RAY DIFFRACTION2{A|64 - 77}
3X-RAY DIFFRACTION3{A|78 - 95}
4X-RAY DIFFRACTION4{A|96 - 137}
5X-RAY DIFFRACTION5{A|138 - 172}
6X-RAY DIFFRACTION6{A|173 - 204}
7X-RAY DIFFRACTION7{A|205 - 219}
8X-RAY DIFFRACTION8{A|220 - 307}
9X-RAY DIFFRACTION9{A|308 - 333}
10X-RAY DIFFRACTION10{A|334 - 345}

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