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- PDB-8aau: LIM Domain Kinase 1 (LIMK1) bound to LIMKi3 -

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Basic information

Entry
Database: PDB / ID: 8aau
TitleLIM Domain Kinase 1 (LIMK1) bound to LIMKi3
ComponentsLIM domain kinase 1
KeywordsTRANSFERASE / Kinase Small-molecule inhibitor CFL-1 Actin cytoskeleton dynamics
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion ...positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / positive regulation of axon extension / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / heat shock protein binding / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / nervous system development / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / nuclear speck / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / metal ion binding / nucleus / 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 / PDZ superfamily ...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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-LH0 / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsMathea, S. / Salah, E. / Hanke, T. / Knapp, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2022
Title: Development and Characterization of Type I, Type II, and Type III LIM-Kinase Chemical Probes.
Authors: Hanke, T. / Mathea, S. / Woortman, J. / Salah, E. / Berger, B.T. / Tumber, A. / Kashima, R. / Hata, A. / Kuster, B. / Muller, S. / Knapp, S.
History
DepositionJul 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8017
Polymers35,9951
Non-polymers8066
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-40 kcal/mol
Surface area14130 Å2
Unit cell
Length a, b, c (Å)85.668, 85.668, 182.108
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11L-884-

HOH

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Components

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Protein , 1 types, 1 molecules L

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


Mass: 35994.773 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 105 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-LH0 / ~{N}-[5-[2-[2,6-bis(chloranyl)phenyl]-5-[bis(fluoranyl)methyl]pyrazol-3-yl]-1,3-thiazol-2-yl]-2-methyl-propanamide


Mass: 431.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14Cl2F2N4OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M acetate pH 4.5, 0.2 M lithium sulfate, 12% PEG8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.74→68.71 Å / Num. obs: 41448 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 33.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.01899 / Net I/σ(I): 16.7
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2391 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4039 / CC1/2: 0.913 / % possible all: 99.98

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NXD

5nxd


Resolution: 1.74→68.71 Å / SU ML: 0.1721 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3019
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 2043 4.93 %
Rwork0.2114 39405 -
obs0.2128 41448 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.7 Å2
Refinement stepCycle: LAST / Resolution: 1.74→68.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2273 0 47 99 2419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01012390
X-RAY DIFFRACTIONf_angle_d1.0783247
X-RAY DIFFRACTIONf_chiral_restr0.0687351
X-RAY DIFFRACTIONf_plane_restr0.011438
X-RAY DIFFRACTIONf_dihedral_angle_d5.6024344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.28721170.29012580X-RAY DIFFRACTION99.96
1.78-1.820.29291340.25662575X-RAY DIFFRACTION99.96
1.82-1.870.28981280.23042570X-RAY DIFFRACTION100
1.87-1.930.27041290.22372574X-RAY DIFFRACTION99.96
1.93-1.990.24481480.23312584X-RAY DIFFRACTION99.96
1.99-2.060.29551490.24812564X-RAY DIFFRACTION100
2.06-2.140.2541410.22812585X-RAY DIFFRACTION100
2.14-2.240.22371260.21412597X-RAY DIFFRACTION100
2.24-2.360.22341220.2132619X-RAY DIFFRACTION99.96
2.36-2.510.27631360.22862620X-RAY DIFFRACTION100
2.51-2.70.2681250.23012634X-RAY DIFFRACTION100
2.7-2.970.23541670.23342621X-RAY DIFFRACTION100
2.97-3.40.23891380.21942660X-RAY DIFFRACTION100
3.4-4.290.21251420.19142722X-RAY DIFFRACTION100
4.29-68.710.23291410.19092900X-RAY DIFFRACTION100
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)
14.13696179659-1.24311520015-0.4456124911441.79819390453-0.6281239826330.447993424215-0.05953138057540.4811024494230.2963756146990.01375720825090.03604112246620.0683210639205-0.0662639188352-0.11489349190.008169822317740.336706008162-0.0566560357672-0.007863641249420.3529848745830.06530908020780.21778885291-19.920878789844.5774757444-12.8924163535
24.1671348922-0.03020764882731.469600921021.58641985484-0.2573109077012.32079671964-0.1287038966660.142634051973-0.4445702814640.02885056485130.08156067992670.012621845531-0.007295422400060.1064767965240.04536759178510.270799100645-0.02352757592210.03787940998680.2319228037830.003642544121450.238241048818-3.7030472014426.6781379916-4.86130710267
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: L / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'L' and (resid 328 through 433 )328 - 4331 - 106
22chain 'L' and (resid 434 through 634 )434 - 634107 - 291

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