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- PDB-5nxd: LIM Domain Kinase 2 (LIMK2) In Complex With TH-300 -

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Basic information

Entry
Database: PDB / ID: 5nxd
TitleLIM Domain Kinase 2 (LIMK2) In Complex With TH-300
ComponentsLIM domain kinase 2
KeywordsTRANSFERASE / Kinase Actin cytoskeleton Inhibitor DFG-out
Function / homology
Function and homology information


cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / EPHB-mediated forward signaling / positive regulation of protein localization to nucleus ...cornea development in camera-type eye / establishment of vesicle localization / head development / astral microtubule organization / negative regulation of cilium assembly / cis-Golgi network / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / EPHB-mediated forward signaling / positive regulation of protein localization to nucleus / mitotic spindle / actin cytoskeleton organization / spermatogenesis / 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 phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-9D8 / LIM domain kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMathea, S. / Salah, E. / Hanke, T. / Newman, J.A. / Oerum, S. / Wang, D. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. ...Mathea, S. / Salah, E. / Hanke, T. / Newman, J.A. / Oerum, S. / Wang, D. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. / Knapp, S.
CitationJournal: To Be Published
Title: LIM Domain Kinase 2 (LIMK2)In Complex With TH-300
Authors: Mathea, S. / Salah, E. / Hanke, T. / Newman, J.A. / Oerum, S. / Wang, D. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. / Knapp, S.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: LIM domain kinase 2
B: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6096
Polymers69,5992
Non-polymers1,0104
Water2,396133
1
A: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3053
Polymers34,8001
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIM domain kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3053
Polymers34,8001
Non-polymers5052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.275, 66.605, 82.124
Angle α, β, γ (deg.)90.00, 97.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein LIM domain kinase 2 / LIMK-2


Mass: 34799.707 Da / Num. of mol.: 2 / Fragment: UNP residues 330-632
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK2 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53671, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-9D8 / 4-[(3-chlorophenyl)sulfamoyl]-~{N}-(phenylmethyl)-~{N}-propyl-benzamide


Mass: 442.958 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23ClN2O3S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M bis-tris-propane pH 7.5 0.2 M Na2SO4 10% ethylene glycol 17% PEG3.35K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→66.61 Å / Num. obs: 51845 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2625 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TPT

4tpt


Resolution: 1.9→66.61 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.568 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23042 2594 5 %RANDOM
Rwork0.19485 ---
obs0.19666 49231 97.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0 Å20.03 Å2
2--0.53 Å20 Å2
3----0.11 Å2
Refinement stepCycle: 1 / Resolution: 1.9→66.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4214 0 68 133 4415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194396
X-RAY DIFFRACTIONr_bond_other_d0.0020.024127
X-RAY DIFFRACTIONr_angle_refined_deg1.91.9675959
X-RAY DIFFRACTIONr_angle_other_deg1.07839545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9535540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11723.977171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47615731
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881516
X-RAY DIFFRACTIONr_chiral_restr0.1130.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215034
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02906
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_it2.6292.8022172
X-RAY DIFFRACTIONr_mcbond_other2.6282.8022173
X-RAY DIFFRACTIONr_mcangle_it3.734.1872703
X-RAY DIFFRACTIONr_mcangle_other3.7294.1872704
X-RAY DIFFRACTIONr_scbond_it3.1533.0682224
X-RAY DIFFRACTIONr_scbond_other3.1523.0672225
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6974.493256
X-RAY DIFFRACTIONr_long_range_B_refined5.93733.5234913
X-RAY DIFFRACTIONr_long_range_B_other5.93633.5234914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.904→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 188 -
Rwork0.276 3709 -
obs--99.8 %

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