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- PDB-4yzn: Humanized Roco4 bound to Compound 19 -

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Basic information

Entry
Database: PDB / ID: 4yzn
TitleHumanized Roco4 bound to Compound 19
ComponentsProbable serine/threonine-protein kinase roco4
KeywordsTRANSFERASE / Roco-Protein / Kinase / LRRK2 / Inhibitor / Roco4
Function / homology
Function and homology information


sorocarp stalk development / Regulation of necroptotic cell death / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity ...sorocarp stalk development / Regulation of necroptotic cell death / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / 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 kinase activity / protein serine kinase activity / GTP binding / signal transduction / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / : / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / : / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Trp-Asp (WD) repeats circular profile. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4K5 / Probable serine/threonine-protein kinase roco4
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsGilsbach, B.K. / Messias, A.C. / Ito, G. / Sattler, M. / Alessi, D.R. / Wittinghofer, A. / Kortholt, A.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
MJFF for Parkinson Research Netherlands
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structural Characterization of LRRK2 Inhibitors.
Authors: Gilsbach, B.K. / Messias, A.C. / Ito, G. / Sattler, M. / Alessi, D.R. / Wittinghofer, A. / Kortholt, A.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Oct 19, 2016Group: Refinement description
Revision 1.3Jan 10, 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
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: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0042
Polymers32,5491
Non-polymers4551
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.400, 42.400, 326.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1614-

HOH

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Components

#1: Protein Probable serine/threonine-protein kinase roco4 / Ras of complex proteins and C-terminal of roc 4


Mass: 32548.508 Da / Num. of mol.: 1
Fragment: Humanized Roco4 Kinase Domain, UNP residues 1019-1292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: roco4, DDB_G0288251 / Plasmid: pGEX4T1 NTev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3
References: UniProt: Q6XHB2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4K5 / (4-{[4-(cyclopropylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-2-fluoro-5-methoxyphenyl)(morpholin-4-yl)methanone


Mass: 455.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21F4N5O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM 1,3-bis(tris(hydroxymethyl)methylamino)propane pH 8.5 200mM Na/K tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99995 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 1.55→37.64 Å / Num. obs: 45260 / % possible obs: 99.7 % / Redundancy: 3.4 % / Net I/σ(I): 8.51
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0093refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f0f

4f0f


Resolution: 1.55→37.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.313 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21595 2262 5 %RANDOM
Rwork0.18742 ---
obs0.18887 45260 99.91 %-
all-45260 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.239 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.55→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2161 0 32 214 2407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222312
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6131.9973150
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9995298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4724.12497
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09315407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2121513
X-RAY DIFFRACTIONr_chiral_restr0.1820.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211741
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 132 -
Rwork0.27 2740 -
obs--99.83 %

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