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- PDB-4yzm: Humanized Roco4 bound to LRRK2-In1 -

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Basic information

Entry
Database: PDB / ID: 4yzm
TitleHumanized Roco4 bound to LRRK2-In1
ComponentsProbable serine/threonine-protein kinase roco4
KeywordsTRANSFERASE / Roco-Protein / Kinase / LRRK2 / Inhibitor
Function / homology
Function and homology information


sorocarp stalk development / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity ...sorocarp stalk development / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine 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, 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 ...C-terminal of Roc (COR) domain / C-terminal of Roc, COR, 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / WD40/YVTN repeat-like-containing domain superfamily / Winged helix-like DNA-binding 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-4K4 / Probable serine/threonine-protein kinase roco4
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGilsbach, B.K. / Messias, A.C. / Ito, G. / Sattler, M. / Alessi, D.R. / Wittinghofer, A. / Kortholt, A.
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 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Probable serine/threonine-protein kinase roco4
B: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2876
Polymers65,0972
Non-polymers1,1904
Water64936
1
A: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1433
Polymers32,5491
Non-polymers5952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1433
Polymers32,5491
Non-polymers5952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.030, 89.070, 177.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 2 / Fragment: 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 BL21(DE3) (bacteria)
References: UniProt: Q6XHB2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4K4 / 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 570.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H38N8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
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), 200 mM Na/K tartrate, 11% (m/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97889 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 3→44.43 Å / Num. obs: 13688 / % possible obs: 99.3 % / Redundancy: 2.9 % / Net I/σ(I): 10.62
Reflection shellResolution: 3→3.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.36 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f0f

4f0f


Resolution: 3→44.43 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.843 / SU B: 38.046 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 719 5 %RANDOM
Rwork0.19556 ---
obs0.19982 13688 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 86 36 4325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9432.0036108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.124.271199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16315792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8971524
X-RAY DIFFRACTIONr_chiral_restr0.1420.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213397
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: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 46 -
Rwork0.263 886 -
obs--99.68 %
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)
11.42870.78-0.65151.6092-0.22031.57440.1326-0.15860.01920.2589-0.1101-0.03030.08530.037-0.02260.06750.0043-0.00560.0923-0.02190.0828-20.83660.0293-31.7111
21.44130.28280.30381.54530.35712.07930.1503-0.0382-0.10190.2039-0.0977-0.0238-0.1111-0.0663-0.05260.0610.00150.01030.05670.00610.0645-1.033941.8263-15.1241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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