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- PDB-5nxc: LIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736 -

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Basic information

Entry
Database: PDB / ID: 5nxc
TitleLIM Domain Kinase 1 (LIMK1) In Complex With PF-00477736
ComponentsLIM domain kinase 1
KeywordsTRANSFERASE / Kinase Actin cytoskeleton Inhibitor
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / axon extension / stress fiber assembly / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / ubiquitin ligase inhibitor activity / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction ...positive regulation of actin filament bundle assembly / RHO GTPases Activate ROCKs / Sema4D induced cell migration and growth-cone collapse / axon extension / stress fiber assembly / RHO GTPases activate PAKs / Fc-gamma receptor signaling pathway involved in phagocytosis / ubiquitin ligase inhibitor activity / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / positive regulation of axon extension / positive regulation of stress fiber assembly / heat shock protein binding / EPHB-mediated forward signaling / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / nervous system development / lamellipodium / actin cytoskeleton organization / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 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 / postsynapse / protein kinase activity / neuron projection / nuclear speck / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ubiquitin protein ligase binding / glutamatergic synapse / signal transduction / ATP binding / metal ion binding / nucleus / membrane / cytosol / 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-9DB / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMathea, S. / Salah, E. / Pike, A.C.W. / Bushell, S. / Carpenter, E.P. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.N. / Knapp, S.
CitationJournal: To Be Published
Title: LIM Domain Kinase (LIMK1) In Complex With PF-00477736
Authors: Mathea, S. / Salah, E. / Pike, A.C.W. / Bushell, S. / Carpenter, E.P. / 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
L: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4142
Polymers35,9951
Non-polymers4191
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.387, 95.836, 84.392
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 35994.773 Da / Num. of mol.: 1 / Fragment: UNP residues 330-637
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53667, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-9DB / (2~{R})-2-azanyl-2-cyclohexyl-~{N}-[2-(1-methylpyrazol-4-yl)-9-oxidanylidene-3,10,11-triazatricyclo[6.4.1.0^{4,13}]trideca-1,4,6,8(13),11-pentaen-6-yl]ethanamide


Mass: 419.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H25N7O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.32 Å3/Da / Density % sol: 46.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7.0 0.2 M MgCl2 10% PEG8K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.25→84.39 Å / Num. obs: 17463 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 6.3
Reflection shellResolution: 2.25→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 857 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YI6

1yi6


Resolution: 2.25→64.97 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.866 / SU B: 8.153 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.248 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29837 815 4.7 %RANDOM
Rwork0.23911 ---
obs0.24188 16629 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.185 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å2-0 Å2-0 Å2
2--1.96 Å20 Å2
3----1.35 Å2
Refinement stepCycle: 1 / Resolution: 2.25→64.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 31 44 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192224
X-RAY DIFFRACTIONr_bond_other_d0.0020.022057
X-RAY DIFFRACTIONr_angle_refined_deg1.7491.9553022
X-RAY DIFFRACTIONr_angle_other_deg1.08734716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg75272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15723.22996
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78815351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9891514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212606
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
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_it2.2472.8731095
X-RAY DIFFRACTIONr_mcbond_other2.2462.8731096
X-RAY DIFFRACTIONr_mcangle_it3.5324.31364
X-RAY DIFFRACTIONr_mcangle_other3.5314.31365
X-RAY DIFFRACTIONr_scbond_it2.2942.961129
X-RAY DIFFRACTIONr_scbond_other2.2932.9611130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5474.3681659
X-RAY DIFFRACTIONr_long_range_B_refined5.05222.042468
X-RAY DIFFRACTIONr_long_range_B_other5.05422.0322457
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.246→2.304 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 58 -
Rwork0.271 1186 -
obs--99.92 %

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