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- PDB-4wsq: Crystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) i... -

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Basic information

Entry
Database: PDB / ID: 4wsq
TitleCrystal Structure of Adaptor Protein 2 Associated Kinase (AAK1) in complex with small molecule inhibitor
ComponentsAP2-associated protein kinase 1
KeywordsTRANSFERASE / kinase / small-molecule / catalytic domain / protein kinase / protein binding / protein kinase inhibitors
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 / presynapse / Clathrin-mediated endocytosis / protein stabilization / non-specific serine/threonine protein kinase / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / 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
K-252A / AP2-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSorrell, F.J. / Elkins, J.M. / Krojer, T. / Williams, E. / Abdul, K. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. ...Sorrell, F.J. / Elkins, J.M. / Krojer, T. / Williams, E. / Abdul, K. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2016
Title: Family-wide Structural Analysis of Human Numb-Associated Protein Kinases.
Authors: Sorrell, F.J. / Szklarz, M. / Abdul Azeez, K.R. / Elkins, J.M. / Knapp, S.
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Mar 9, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _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: AP2-associated protein kinase 1
B: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,87811
Polymers71,4882
Non-polymers1,3899
Water5,134285
1
A: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4706
Polymers35,7441
Non-polymers7265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AP2-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4085
Polymers35,7441
Non-polymers6644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.660, 71.320, 183.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSLYSchain AAA29 - 3451 - 317
2ALAALAchain BBB33 - 3425 - 314
Detailsunit 1

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Components

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


Mass: 35744.090 Da / Num. of mol.: 2 / Fragment: kinase domain, UNP residues 29-345
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AAK1, KIAA1048 / Plasmid: pNIC-CTH0 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): R3
References: UniProt: Q2M2I8, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-KSA / K-252A


Mass: 467.473 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H21N3O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.005M zinc acetate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.95→56.33 Å / Num. obs: 66564 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.05 / Net I/σ(I): 8.3 / Num. measured all: 310951 / Scaling rejects: 32
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.95-24.81.0942.12093343790.7940.535100
9.15-56.334.20.0382030757380.9970.02198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimless0.2.17data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2buj

2buj


Resolution: 1.95→56.325 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 3225 4.85 %Random selection
Rwork0.1809 63212 --
obs0.1821 66437 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.15 Å2 / Biso mean: 43.5603 Å2 / Biso min: 20.97 Å2
Refinement stepCycle: final / Resolution: 1.95→56.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4841 0 80 285 5206
Biso mean--28.52 45.56 -
Num. residues----627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135101
X-RAY DIFFRACTIONf_angle_d1.2736967
X-RAY DIFFRACTIONf_chiral_restr0.063785
X-RAY DIFFRACTIONf_plane_restr0.007896
X-RAY DIFFRACTIONf_dihedral_angle_d12.841829
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2775X-RAY DIFFRACTION5.886TORSIONAL
12B2775X-RAY DIFFRACTION5.886TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97910.35231250.303927312856100
1.9791-2.010.33281590.29626612820100
2.01-2.0430.28381350.281727302865100
2.043-2.07820.27421560.253926972853100
2.0782-2.1160.30641320.240327082840100
2.116-2.15670.29061350.231727302865100
2.1567-2.20080.2631350.226127222857100
2.2008-2.24860.25921480.204126882836100
2.2486-2.30090.23731450.187927292874100
2.3009-2.35850.24361580.190626942852100
2.3585-2.42220.22321490.186427032852100
2.4222-2.49350.21191390.181827162855100
2.4935-2.5740.22911350.17527402875100
2.574-2.6660.22561450.17727682913100
2.666-2.77270.23341340.180827272861100
2.7727-2.89890.22551650.18427222887100
2.8989-3.05170.19691430.181527482891100
3.0517-3.24290.1871020.18628242926100
3.2429-3.49330.19811180.187427802898100
3.4933-3.84470.19511450.160827842929100
3.8447-4.40090.16161620.151527752937100
4.4009-5.54390.15891250.14528542979100
5.5439-56.34860.17561350.16482981311699
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)
10.87040.4837-0.0842.2357-0.67641.7816-0.0530.0319-0.0481-0.07310.0063-0.02490.01850.04380.03840.34440.0304-0.0030.1873-0.01960.24843.0307-14.7644-41.5051
21.1956-0.25140.75182.0424-0.32771.7085-0.12120.16140.1573-0.2306-0.0452-0.10990.03080.0650.14740.4099-0.01460.01510.30380.03750.272-3.4734-11.9255-92.291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 29:345)A29 - 345
2X-RAY DIFFRACTION2(chain B and resseq 33:342)B33 - 342

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